Registered Reports Peer Review: Stage 1 & 2 Explained

What Are Registered Reports in Peer Review? Stage 1, Stage 2, Benefits, and Examples

Traditional peer review usually takes place after researchers have completed a study, analyzed the data, and written a manuscript. Reviewers then evaluate the research findings, methodology, originality, and scientific contribution before a journal makes its publication decision.

However, this approach can create a problem: research with statistically significant or unexpected findings may attract more attention than equally rigorous studies producing null or negative results.

Registered Reports offer a different approach to peer review.

A Registered Report is a scholarly article format in which the research question, study design, and planned analyses undergo peer review before the principal data collection and analysis take place.

If the proposed study meets the journal's standards, the authors receive in-principle acceptance (IPA). This means the journal commits to publishing the completed study if the researchers follow the approved protocol, satisfy specified quality checks, and interpret the findings appropriately.

Importantly, publication does not depend on whether the study confirms the original hypothesis.

This two-stage review model aims to strengthen research methods and reduce bias related to the direction or statistical significance of findings.

In this guide, we explain how Registered Reports peer review works, what happens during Stage 1 and Stage 2, how it differs from traditional review, and the benefits and limitations researchers should understand.

What Are Registered Reports?

Registered Reports are a publishing format that evaluates the scientific importance and methodological quality of a proposed study before the main research outcomes are known.

Instead of submitting a completed manuscript containing results and discussion, researchers initially submit a detailed study protocol.

The proposal typically includes the research question, theoretical background, hypotheses where applicable, study design, sampling strategy, planned analyses, and quality-control procedures.

Editors and reviewers evaluate whether the proposed methods are capable of answering the research question.

If the protocol passes Stage 1 review, the journal grants in-principle acceptance.

Researchers then complete the approved study and submit a full manuscript for Stage 2 evaluation.

A Registered Report can report findings that support the hypothesis, contradict it, or show no statistically significant effect.

The key requirement is that the research meets the agreed scientific standards.

This format is particularly relevant to confirmatory and hypothesis-driven research, although individual journals may also accept replication studies or other eligible designs.

How Does Registered Reports Peer Review Work?

Registered Reports use a two-stage review process.

The main difference from conventional peer review is that the initial editorial commitment is made before the study results are known.

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The format does not mean that reviewers automatically approve the finished study.

It means the principal publication decision is separated from whether the results support the researchers' expectations.

Stage 1 Registered Reports: Review Before Data Collection

Stage 1 is the defining feature of the Registered Reports model.

At this stage, authors submit a detailed research proposal before collecting the principal study data.

The manuscript usually contains an introduction and methods section but does not contain the results of the proposed main study.

Pilot data may be included where permitted or required.

What Does a Stage 1 Submission Include?

According to Nature Human Behaviour's Registered Reports guidelines, a Stage 1 submission typically describes:

• The research question and its scientific importance.
• Theoretical background and relevant literature.
• Hypotheses or clearly defined research objectives.
• Experimental or observational design.
• Participant or sample selection procedures.
• Inclusion and exclusion criteria.
• Planned data collection methods.
• Statistical or other analysis procedures.
• Sample size justification and statistical power, when applicable.
• Outcome-neutral quality checks.
• Pilot evidence, when relevant.

The exact requirements vary by journal.

The protocol should contain enough detail for reviewers to evaluate whether the planned research can produce informative evidence.

What Do Reviewers Evaluate During Stage 1?

Stage 1 reviewers focus on scientific reasoning and methodological rigor.

They assess whether the research question is meaningful and whether the proposed methods can answer it.

For example, a reviewer may examine whether the sample size is sufficient to detect an effect of scientific interest.

Another reviewer may question whether the planned statistical model is suitable for the data structure.

Reviewers can also identify confounding factors, missing controls, or weaknesses in the proposed analysis plan.

Because the results are not yet known, criticism can focus on improving the study before substantial research resources are committed.

What Happens After Stage 1 Review?

The journal may reject the proposal, request revisions, or grant in-principle acceptance.

A Stage 1 revision may require substantial methodological changes.

For example, reviewers may request a clearer primary outcome, revised sampling procedures, or stronger quality-control measures.

Once these concerns are resolved and the journal's standards are met, the manuscript may receive in-principle acceptance.

What Is In-Principle Acceptance in Registered Reports?

In-principle acceptance (IPA) is a conditional commitment by a journal to publish a Registered Report after the study is completed.

The commitment is made before the principal study results are known.

This helps separate publication decisions from whether findings are statistically significant or consistent with the original hypothesis.

However, IPA is not unconditional acceptance.

The authors must satisfy the journal's requirements.

These generally include following the approved research protocol, completing prespecified quality checks, reporting the planned analyses, and presenting conclusions supported by the evidence.

If researchers substantially deviate from the accepted protocol without appropriate editorial approval, the journal may reconsider the publication commitment.

Nature Human Behaviour explicitly states that significant unauthorized protocol changes can lead to rejection at Stage 2.

The distinction matters: Registered Reports provide results-independent conditional acceptance, not immunity from methodological or ethical scrutiny.

What Happens After In-Principle Acceptance?

After receiving IPA, researchers normally register the approved protocol in a recognized repository according to the journal's policies.

Some journals permit the protocol to remain under embargo until the completed study is submitted or published.

Researchers then conduct the research in accordance with the approved procedures.

For example, a study investigating whether a teaching intervention improves student performance would follow the previously reviewed sampling, intervention, outcome measurement, and analysis plan.

The researchers should document their methods and maintain the required data and research records.

If an unexpected technical problem makes an approved procedure impossible, the authors should contact the journal editor and explain the proposed modification.

Depending on the journal, a minor amendment may be permitted.

Major changes may require renewed Stage 1 assessment or another publication route.

Authors should not quietly alter approved analyses after observing the results.

Stage 2 Registered Reports: Review After the Study

Stage 2 begins after the researchers complete the study.

The authors prepare a full manuscript containing the results, discussion, and conclusions.

The journal then evaluates whether the completed research meets the conditions established at Stage 1.

What Do Reviewers Check During Stage 2?

Stage 2 reviewers typically assess five main areas.

Protocol adherence: Did the authors follow the approved research procedures?

Prespecified quality checks: Did the study satisfy the conditions required for interpreting the results?

Complete reporting: Were the planned analyses and outcomes reported appropriately?

Exploratory analyses: Are additional, unregistered analyses identified and scientifically justified?

Interpretation: Do the conclusions accurately reflect the evidence?

The reviewers are not supposed to reject the study merely because the findings are statistically insignificant, surprising, or inconsistent with the researchers' original prediction.

For example, if a rigorously conducted experiment finds no evidence that a proposed intervention improves performance, that result can still qualify for publication.

The scientific value of the study depends on the quality of the research question, methods, and evidence—not on producing a desired result.

Stage 1 vs. Stage 2 Registered Reports

The two stages are complementary.

Stage 1 evaluates whether the research is designed appropriately.

Stage 2 evaluates whether the completed work fulfills that design and supports the conclusions presented.

Registered Reports vs. Traditional Peer Review

Traditional peer review and Registered Reports both involve expert evaluation, but they differ in timing and editorial decision-making.

Registered Reports do not eliminate ordinary scientific review.

Instead, they reorganize review so that the study design is evaluated before its outcomes are available.

Registered Reports vs. Preregistration

Registered Reports and preregistration are closely related but not identical.

Preregistration means documenting a research plan before conducting the relevant study or analysis.

A preregistration may describe hypotheses, methods, outcomes, and statistical procedures.

It does not automatically require a journal editor or external reviewers to evaluate the plan.

Registered Reports add a formal peer-review process and potential in-principle acceptance before the study is completed.

A preregistered study is not automatically a Registered Report.

Similarly, depositing a protocol in an online repository does not mean the study has received Stage 1 peer-review approval.

Real-World Examples of Registered Reports

Several established publishers offer Registered Reports as an article format.

Example 1: Nature Human Behaviour

Nature Human Behaviour provides detailed Stage 1 and Stage 2 guidelines for Registered Reports.

At Stage 1, editors and reviewers assess the theoretical importance, hypotheses, research methodology, planned analyses, and feasibility of the study.

Proposals meeting its editorial criteria can receive in-principle acceptance.

Researchers then conduct the approved study and prepare a completed manuscript.

At Stage 2, reviewers evaluate protocol adherence, quality checks, exploratory analyses, and interpretation.

The journal states that editorial decisions at this stage should not depend on the perceived novelty or statistical significance of the resulting findings.

Example 2: Scientific Reports

Scientific Reports also accepts Registered Reports.

Its model includes protocol evaluation before the main study and a subsequent review of the completed manuscript.

The journal considers scientifically justified replication studies within the format.

This demonstrates how Registered Reports can support studies aimed at testing whether previously reported findings can be reproduced.

Replication results remain informative even when they do not confirm the original effect.

Example 3: Nature Communications

Nature Communications offers Registered Reports with Stage 1 evaluation and subsequent Stage 2 review.

After in-principle acceptance, the approved protocol is registered in an appropriate repository.

The completed manuscript must include the relevant protocol-registration information.

Its policy emphasizes completing approved methods, passing quality checks, and interpreting the results defensibly.

Example 4: A Hypothetical Educational Research Study

Consider a research project titled:

"Does AI-Assisted Feedback Improve Academic Writing Among University Students?"

The researchers want to compare students receiving AI-assisted feedback with students receiving conventional instructor feedback.

Before recruiting participants, they submit a Stage 1 Registered Report.

The protocol describes the participant eligibility criteria, assignment procedures, writing assessment measures, proposed sample size, and planned statistical tests.

Reviewers examine whether the study can meaningfully evaluate the research question.

They recommend clarifying how writing quality will be assessed and strengthening the sample size justification.

The researchers revise the protocol and receive in-principle acceptance.

After conducting the study, they find that the difference between the groups is smaller than anticipated and is not statistically significant.

They nevertheless submit the completed manuscript.

At Stage 2, reviewers confirm that the approved procedures were followed and assess whether the authors' interpretation reflects the results.

If the study satisfies the journal's requirements, it can be published despite not supporting the original hypothesis.

This example is fictional but illustrates the essential logic of Registered Reports.

What Are the Benefits of Registered Reports?

Registered Reports offer several potential advantages for research quality and scholarly publishing.

1. Reduce Publication Bias

Publication bias occurs when studies with certain results are more likely to appear in the published literature.

Research with statistically significant or positive findings may receive disproportionate attention.

Registered Reports reduce this incentive by establishing a conditional publication commitment before the results are known.

This means a scientifically rigorous study can be published even when its findings do not support the original hypothesis.

2. Improve Research Design Before Data Collection

Reviewers can identify methodological weaknesses when corrections are still practical.

For example, they may recommend a more appropriate statistical model or stronger outcome measurement.

This can prevent researchers from discovering critical design flaws only after data collection is complete.

3. Encourage Complete Reporting

Researchers commit to reporting the prespecified analyses and relevant outcomes.

This can make it harder to selectively emphasize only favorable results.

Transparent reporting also helps readers distinguish planned analyses from exploratory findings.

4. Reduce Incentives for Questionable Research Practices

Registered Reports aim to discourage practices such as selectively reporting outcomes, repeatedly testing analyses until statistical significance appears, or presenting data-driven hypotheses as if they were predicted in advance.

These practices are often described using terms such as p-hacking and HARKing.

The registered protocol provides a reference against which later reporting can be assessed.

5. Support Replication Research

Replication studies can receive a publication commitment based on the significance and methodological quality of the proposed test.

This reduces dependence on whether the replication produces the same result as the original study.

6. Increase Research Transparency

Readers can compare the approved research plan with the completed study.

This makes it easier to understand which analyses were specified in advance and which were developed later.

7. Encourage More Informative Null Results

Null results can help refine theories, rule out effects of meaningful size, or identify conditions under which previous findings do not generalize.

Registered Reports provide a publishing route in which the value of those results does not depend solely on statistical significance.

What Does Research Say About Registered Reports?

Published research provides some evidence that Registered Reports can improve research practices, although the evidence is not uniform across every field.

A 2021 study published in Nature Human Behaviour compared 29 published Registered Reports with 57 conventional comparison papers from psychology and neuroscience.

A group of 353 researchers evaluated the papers using multiple criteria.

Registered Reports scored higher on several measures, including methodological rigor, analytical rigor, and overall quality.

The findings offer encouraging evidence for the model, but they do not demonstrate that Registered Reports are superior in all disciplines or circumstances.

Another 2021 study examined positive findings in conventional psychology papers and Registered Reports.

The researchers found that 96% of first hypotheses in the sampled conventional reports received positive support, compared with 44% in Registered Reports.

These differences are consistent with concerns about selective publication and reporting.

However, factors such as study selection and research practices may also contribute to differences between publication formats.

More recently, a comparative study published in American Psychologist examined matched Registered Reports and conventional research papers.

It found evidence of reduced publication bias against null findings and greater transparency in methods and data, while also identifying differences in citation performance.

Together, these studies suggest that Registered Reports can support important aspects of research rigor, but they should not be presented as a perfect solution to every publishing problem.

What Are the Limitations of Registered Reports?

Registered Reports also introduce practical and methodological challenges.

1. Stage 1 Review Can Require Substantial Preparation

Authors must develop detailed research methods and analysis plans before beginning the principal study.

This can require considerable time and expertise.

2. Research Timelines May Become Longer

Stage 1 review and possible revisions occur before the main study begins.

This can delay data collection, especially when reviewers request major methodological changes.

3. Some Research Questions Are Difficult to Specify Fully in Advance

Registered Reports are particularly suitable for confirmatory studies.

Highly exploratory research may require flexibility that is difficult to capture in a detailed predetermined protocol.

Not every journal offers a format suitable for every research design.

4. Unexpected Problems May Require Protocol Amendments

Equipment failures, recruitment difficulties, or unforeseen analytical issues may require modifications.

Authors must manage these changes transparently and seek editorial approval when required.

5. In-Principle Acceptance Is Conditional

A journal may still reject a completed manuscript if authors fail to follow the approved procedures, do not meet required quality checks, or make conclusions unsupported by the evidence.

6. Journal Policies Differ

Submission requirements, data-sharing rules, eligible methods, and amendment procedures vary among journals.

Authors need to read the instructions for the particular publication.

7. The Format Does Not Eliminate Every Form of Research Bias

Reviewers can still disagree about methods or theoretical importance.

Authors may also face practical barriers involving resources, recruitment, or the feasibility of a proposed study.

Registered Reports address certain incentives and practices, not every source of research error.

Can Registered Reports Include Exploratory Analyses?

Yes.

Registered Reports generally allow exploratory analyses, provided they are clearly distinguished from the analyses approved at Stage 1.

For example, the registered protocol may specify a primary comparison between two treatment conditions.

After data collection, researchers may notice an unexpected pattern involving participant age.

They may investigate that pattern through an additional exploratory analysis.

However, the authors should identify the analysis as exploratory rather than present it as a prespecified hypothesis test.

Nature Human Behaviour explicitly permits additional unregistered analyses when they are appropriately justified and reported.

The distinction between confirmatory and exploratory findings is important for accurate interpretation.

Can Authors Change a Registered Report Protocol?

Changes may be possible, but they require careful management.

A minor adjustment may be necessary because of unforeseen circumstances.

For example, researchers might need to replace a discontinued measurement instrument with an appropriate alternative.

They should contact the handling editor and explain the proposed modification.

Depending on journal policy, the editor may permit the change while retaining in-principle acceptance.

Major methodological changes can require renewed assessment or a new Stage 1 submission.

Authors should not assume that any deviation is acceptable simply because the final results appear scientifically interesting.

Transparency about protocol amendments is essential.

Can a Registered Report Be Rejected After Stage 2?

Yes.

Although in-principle acceptance provides a conditional publication commitment, Stage 2 rejection remains possible.

Examples include serious departures from the approved protocol, failure of required outcome-neutral quality checks, important reporting omissions, or unsupported conclusions.

The conditions differ by journal.

However, a properly conducted study should not be rejected merely because the results are statistically insignificant or contradict the original hypothesis.

This distinction is fundamental to the Registered Reports model.

The purpose is to make publication depend on rigorous research rather than favorable outcomes.

How to Write a Stage 1 Registered Report

Researchers planning a Stage 1 submission should begin by examining the journal's specific Registered Reports instructions.

A typical preparation process includes the following steps.

Step 1: Identify a Suitable Research Question

Choose a clearly defined question that can be addressed through a rigorous planned study.

Explain its scientific relevance.

Step 2: Develop the Theoretical Rationale

Review the relevant literature and explain the basis for the proposed hypotheses or objectives.

Step 3: Specify the Study Design

Describe the procedures, variables, measurement instruments, controls, and data collection strategy.

Step 4: Justify the Sample Size

Provide an appropriate sample size rationale.

When relevant, include a statistical power analysis or Bayesian design justification consistent with journal requirements.

Step 5: Prepare the Analysis Plan

Specify primary outcomes, planned statistical tests, exclusion criteria, and other relevant analytical decisions.

Step 6: Establish Quality Checks

Identify conditions that determine whether the completed study can meaningfully test the research question.

These conditions should not depend on whether the results favor the original hypothesis.

Step 7: Address Ethics and Feasibility

Explain how the study will satisfy research ethics requirements and whether the necessary resources are available.

Step 8: Submit for Stage 1 Review

Upload the protocol and supporting materials according to the journal's requirements.

Be prepared to revise the proposal based on reviewers' methodological concerns.

Registered Reports Stage 1 Checklist

This checklist supports planning but does not replace the requirements of the target journal.

Frequently Asked Questions About Registered Reports

What is a Registered Report in peer review?

A Registered Report is an article format in which a research protocol undergoes peer review before the main study results are known. Successful Stage 1 review can lead to in-principle acceptance.

What are Stage 1 and Stage 2 Registered Reports?

Stage 1 evaluates the proposed research question, methodology, and analysis plan. Stage 2 evaluates the completed study, including protocol adherence, quality checks, results, and interpretation.

What does in-principle acceptance mean?

In-principle acceptance is a conditional commitment to publish a study if the researchers complete the approved procedures and satisfy the journal's scientific and reporting requirements.

Can Registered Reports publish negative results?

Yes. Studies can be published regardless of whether the findings support the hypothesis, provided the approved research and quality conditions are satisfied.

Is preregistration the same as a Registered Report?

No. Preregistration documents a research plan in advance, while Registered Reports add formal journal peer review and potential in-principle acceptance before the main study is completed.

Are Registered Reports peer reviewed twice?

They normally undergo peer review at two distinct stages: first for the proposed protocol and later for the completed manuscript. Each stage may include additional revision rounds.

Can researchers add new analyses after Stage 1?

Yes, in many journals. Additional analyses should be clearly identified as exploratory or unregistered and should not replace required prespecified analyses without appropriate justification.

Can Registered Reports be rejected after in-principle acceptance?

Yes. Stage 2 rejection can occur if the authors do not meet the approved methodological, quality-control, or reporting requirements.

Are Registered Reports suitable for every study?

No. They are especially useful for research with clearly defined questions and prespecified methods. Highly exploratory studies may be less suitable, depending on journal policy.

Why are Registered Reports important?

They allow research quality to be assessed before results are known, potentially reducing publication bias, improving study design, and supporting transparent reporting.

Conclusion

Registered Reports peer review is a two-stage publishing model designed to prioritize scientific questions, methodological rigor, and transparent research practices.

At Stage 1, editors and reviewers evaluate the proposed study before the main results are known.

If the protocol meets the journal's standards, the authors receive in-principle acceptance.

At Stage 2, the completed research is assessed for compliance with the approved protocol, successful completion of required quality checks, and scientifically justified interpretation.

The format allows rigorous studies to be published regardless of whether their results are positive, negative, or statistically significant.

Although Registered Reports require careful planning and can involve additional preparation, they offer an important alternative to conventional results-based publication decisions.

By evaluating research methods before outcomes are known, Registered Reports can contribute to a more transparent, reproducible, and credible scholarly literature.