How to Conduct and Write Registered Reports: Guide for Early-Career and Mid-Career Researchers

The “publish or perish” concept has long bothered researchers, especially those in their early and mid-career stages. Many researchers are often apprehensive of journal acceptance. And considering the high desk rejection rate of 72% reported in The State of Development Journals 2025 [1], this apprehension is valid! However, registered reports can help assuage this worry for authors. Does the term seem unfamiliar? Let’s dive into it to know more.  

What are Registered Reports?

Two Stages in Registered Reports

How to Write Registered Reports

Benefits of Registered Reports

Frequently Asked Questions on Registered Reports

What are Registered Reports?

Registered reports are a type of scientific publication that is peer reviewed before the actual study is conducted. Unlike traditional journal submissions, authors should initially submit the research idea or hypotheses and propose the methodology for testing the hypotheses. This initial report undergoes a peer review, and authors receive an “in-principle acceptance” from the journal. Then, authors proceed to conduct the study as per the approved protocol, report their findings, and submit a complete manuscript which is again peer-reviewed before publication.  

Registered reports have gained prominence over the years, with journals under top publishers like Elsevier, Frontiers, Taylor & Francis, and Journal of Medical Internet Research (JMIR) accepting this format of submission [2]. 

Two Stages in Registered Reports

Conducting registered reports is divided into two stages, and your manuscript undergoes a thorough evaluation in both stages as part of the peer review process. 

Stage 1

In stage 1, you will develop the idea for your research and provide a brief introduction and background for the research along with the methodologies you intend to use for the analysis. There is no data collection at this stage. You simply need to provide research hypothesis that you intend to test.  

Consider this as a proposal for conducting your study. Journals will review your initial submission and determine whether the research idea is worth exploring. Here is what peer reviewers are looking to evaluate: 

• The importance of the research questions. 
• The rationale, logic, and the plausibility of the proposed research hypotheses. 
• The feasibility of the suggested methodology. 
• The adequacy of details in the analytical methods to replicate the proposed experimental procedures. 

Following a thorough assessment, your manuscript may be rejected, returned for revisions, or directly accepted.  

a) If rejected, evaluate the reason for rejection. Your submission perhaps did not match the journal’s aims and scope. See if you can submit it to a different journal. Alternatively, depending on the reasons for rejection, you may choose to submit to the same journal by following the traditional journal submission process. 

b) If the peer reviewers recommended revisions, address these in detail and resubmit your proposal for a second round of evaluation. 

c) If accepted, the journal responds with an “in-principle acceptance (IPA)” letter. This means that your final manuscript will be published by the journal provided your study is conducted by strictly adhering to the approved methods. Note that even a slight deviation from the pre-registered methods without prior approval is likely to result in rejection during the stage 2 submission. 

Stage 2

In stage 2, authors need to submit a complete manuscript reporting the study’s findings and conclusions. Ensure that your data collection and analysis are both conducted according to the standards agreed upon in stage 1 submission. In case you need to deviate from the original protocols, communicate this with the journal and get approval for the modifications. The peer review at this stage is typically conducted by the same reviewers who evaluated your initial submission. However this cannot be guaranteed by the journal as the availability of peer reviewers may vary. 

What do peer reviewers evaluate in stage 2 of registered report submissions? 

• Whether the introduction and methods sections match those of the stage 1 submission. 
• Whether the experimental procedures followed are identical to the pre-registered report. 
• If any ad hoc methodologies were followed, were they approved by the journal, how well are they justified, and whether they are relevant and scientifically accurate. 
• Whether the conclusions of the study align with the reported results. 

Once the peer review is complete, the manuscript is considered ready for journal publication. The IPA ensures that your finalized research paper is accepted and published by the journal. However, peer reviewers at this stage could ask for additional ad hoc tests to verify the results. But the authors are not always obligated to provide this; the decision is at the discretion of the journal editor.  

How to Write Registered Reports

Writing manuscripts for registered reports differ from the process followed for a traditional manuscript preparation [3]. Because the submission happens in two stages, authors need to prepare two distinct manuscripts. While the guidelines vary for different journals, below are the details typically required when submitting a registered report. 

Writing Registered Reports in Stage 1

Stage 1 Manuscript

Your stage 1 manuscript should include the Title, Introduction, and Methods. The Introduction section should highlight the research background and justify the rationale for the research idea. Clearly specify what you wish to achieve with the framed research questions and state your research hypothesis. 

In the Methods section, outline the methodologies, statistical tests (if applicable), experimental procedures, and other relevant data analysis techniques that you intend to use for testing your proposed research hypotheses. Some tips to write the Methods section. 

• Use future tense (e.g., We will use a Bayesian model to evaluate…) in your sentences. 
• Describe the sample data in detail and specify the inclusion/exclusion criteria, if any. 
• Provide a clear analysis pipeline, with a solid research plan and detailed pre-processing steps. 
• Explain the experimental procedures in adequate detail along with precise device names and models. 

Stage 1 Cover Letter

You should prepare a cover letter for stage 1 registered report submission, outlining the scientific case and how it is expected to contribute to the research field. The cover letter should also include details on any approvals you have received, funding information, and the availability of necessary equipment. Provide a feasible timeline as well; it need not be accurate, just an estimate of when you anticipate the study could be completed. 

Writing Registered Reports in Stage 2

Stage 2 Manuscript

After you receive an IPA from the journal following the stage 1 peer review, you need to prepare the final manuscript. But before that, your report must be registered in a publicly available repository (e.g., Open Science Framework) or entered into embargo (view-only link). This is called pre-registration, where you can eventually upload the raw data of your study as well.  

Then, conduct your study (data collection and analysis) by following the methods and experimental procedures that were finalized in the stage 1 manuscript. Proceed to prepare the manuscript as per journal guidelines and add the Results, Discussion, and Conclusions sections. Here are a few key points to note when preparing the stage 2 manuscript. 

• The Manuscript Title, Introduction, and Methods should remain almost the same as what was provided in your stage 1 submission. Minor changes like typographical corrections or addition of new citations to reference works can be made. 
• Avoid modifying the research question or hypothesis midway through the study. Do not deviate from the pre-decided materials and methods. If you do need to deviate, communicate this with the journal and justify why it should be done. Clarify why the previously chosen method was not suited to test the data or mention the non-availability of equipment. You also need to provide raw data, either as part of the supplementary material or in the main manuscript depending on journal’s guidelines. 
• Remember to change your writing to the past tense whenever appropriate (e.g., A Bayesian model was used…). 
• The Results, Discussion, and Conclusions sections must be written as per journal requirements. Stick to facts, avoid exaggerating the implications. In case a specific pre-decided method could not be used for the analysis or if a more robust methodology seemed better suited for the evaluation, explain this modification and highlight the change in the stage 2 registered report. 

Stage 2 Cover Letter

The stage 2 cover letter should primarily focus on how you have adhered to the previously agreed study protocols. If there were deviations, clarify when this was agreed with the journal and why it was done (e.g., unavailability of equipment). Mention where the raw data can be accessed, which is generally available in the repository after pre-registration. 

Benefits of Registered Reports

Registered reports as a publication format benefits both authors and the research community. One major advantage of registered reports is that the acceptance for publication is results-blind. Reviewers evaluate the potential of a research idea rather than identifying whether the results are positive, minimizing publication bias. Because both positive and negative results are published if the IPA is confirmed, authors need not fret about showing only a positive outcome for their hypothesis. 

The second key benefit is the assurance of publication for authors. As long as the research plan approved in stage 1 is followed, authors can stay confident of their work getting published regardless of the outcome of the study. Receiving the IPA also means that your study can be pre-registered, giving your research visibility from the early stages. This can be especially beneficial for early-career researchers (ECRs) as they build their profile in the academic field. 

The two-stage submission calls for a two-stage peer review, providing authors an opportunity to course-correct their research in the early stages if necessary. The feedback from reviewers can set the right foundation for the research, ensuring that high-quality research reaches the audience. 

Frequently Asked Questions on Registered Reports

1. What best describes a registered report?

A registered report is an initial proposal to conduct research, submitted to a journal before the actual commencement of the study. Authors submit research hypotheses plus the methodologies they wish to use for the analysis and await feedback from the journal before deciding to initiate the data collection and analysis. Registered reports are written in two stages, with the first stage focusing on introduction and methods whereas the second stage builds on the initial manuscript by appending it with the results, discussion, and conclusions of the study.  

2. What is in-principle acceptance (IPA)? 

In-principle acceptance (IPA) is the approval given by journals after the stage 1 submission of a registered report, intimating the authors that their research proposal is accepted and they can conduct the next stage of the study. IPA ensures authors that their research paper will be published in the journal regardless of the outcome of the study, provided the analysis follows the pre-decided experimental procedures and adheres to the standards agreed upon in the first stage submission.

3. Are registered reports peer-reviewed?

Yes, registered reports are peer reviewed separately in both the first and second stages. The first stage peer review focuses on assessing the rationale of the proposed research questions and the soundness and feasibility of the methodologies and experimental procedures. In the second stage, peer reviewers evaluate whether the findings were obtained by adhering to the standards approved in the first stage. They also check whether the conclusions of the study align with the reported findings and the hypothesized research questions.  

4. What is the difference between pre-registration and a registered report?

Once you receive the in-principle acceptance (IPA) from the journal, you can pre-register your study by registering your research plan in a repository like the Open Science Framework. The registration may be public or entered into embargo. If your registration is embargoed, your research plan is accessible as a view-only link. Note that the pre-registered plan must be made public after the research is published.  

Registered reports are sort of a continuation of the pre-registration. Once you complete the study as per the standards agreed upon in the IPA, you should submit the stage 2 manuscript in the format required by the journal. Your study gets published as a registered report regardless of the outcome as long as you followed the pre-registered methodologies and experimental procedures.  

5. What are the benefits of registered reports?

Registered reports help minimize publication bias as both positive and negative results get published after authors receive the IPA. The guaranteed publication allows authors to easily navigate the “publish or perish” concept, focusing on conducting the study rather than worrying about the results. The thorough two-stage peer review process followed for registered reports further ensure that high-quality research gets published.  

Want an expert-driven pre-submission check and comprehensive formatting? Check out Editage’s Desk Rejection Shield Service and clear that first hurdle in journal publishing! 

References 

1. The State of Development Journals 2025 https://blogs.worldbank.org/en/impactevaluations/the-state-of-development-journals-2025–quality–acceptance-rate#:~:text=In%20addition%20to%20wanting%20to,varying%20a%20lot%20across%20journals. 

2. Registered reports https://www.cos.io/initiatives/registered-reports

3. Ten simple rules for writing a registered report https://pmc.ncbi.nlm.nih.gov/articles/PMC9612468/