Navigating the Journal Publication Process: A Step-by-Step Guide for Researchers

Publishing in a peer-reviewed journal is a critical step in the research process. It allows your findings to be shared, scrutinised, cited, and built upon by the wider scientific and clinical community. However, for many researchers, especially those publishing for the first time, the journal submission process can feel opaque, complex, and time-consuming.

In this guide, we walk through the key stages of the publication process, offering practical tips to help you prepare your manuscript, choose the right journal, and respond effectively to reviewer feedback.

1. Plan for Journal Publication Early

Successful publication begins well before the writing stage. From the moment you design your study or initiate data collection, keep the eventual manuscript in mind. This includes:

• Identifying the likely audience for your research

• Considering the type of article (e.g., original research, review, case report)

• Maintaining detailed records and pre-specifying your methodology

• Ensuring ethical approval and data transparency

By planning with publication in mind, you avoid many of the delays and pitfalls that arise later.

2. Choose the Right Journal

Selecting the right journal is one of the most important decisions in the process. Factors to consider include:

• Scope and readership: Does the journal regularly publish research like yours?

• Impact factor and indexing: Consider visibility, but balance this with relevance and acceptance likelihood

• Open access vs subscription: Consider funder requirements and article processing charges (APCs)

• Turnaround times: Some journals are faster than others, especially for clinical research or case reports

Study recent articles in your target journal to understand its preferred style, structure, and level of detail.

3. Prepare a Structured Manuscript

Most scientific journals follow the IMRaD structure: Introduction, Methods, Results, and Discussion. Write with clarity, brevity, and objectivity. Key tips:

• Follow the journal’s author guidelines precisely — from formatting to reference style

• Ensure your abstract is concise and accurately reflects your findings

• Use subheadings, figures, and tables to support readability

• Acknowledge limitations transparently

• Include all required statements (e.g., ethics, funding, conflict of interest)

Avoid unnecessary jargon and write for an informed but non-specialist reader.

4. Prepare Supporting Documents

Beyond the main manuscript, you will usually need to submit:

• A cover letter: Briefly explain the significance of your work and why it is suitable for the journal

• Figures and tables: Often uploaded separately in specific formats

• Supplementary data: Detailed tables, protocols, or datasets

• Author contribution and disclosure forms

• Ethics and trial registration statements (if applicable)

Many journals use online submission portals that require each document to be uploaded individually. Prepare these ahead of time to avoid delays.

5. Submit and Track Your Manuscript

Once submitted, the journal will conduct an initial editorial screening. Your manuscript may be desk-rejected if it is outside scope, poorly formatted, or lacks novelty.

If it passes, it moves to peer review — typically involving two or more independent reviewers. This process can take weeks or months, depending on the journal and complexity.

You can usually track the progress via the submission portal. Be patient but proactive — a polite enquiry is acceptable if your manuscript has been under review for more than three months with no update.

6. Responding to Reviewer Comments

Reviewer feedback is a central part of the scientific process. A decision letter will usually recommend:

• Accept (rare on first submission)

• Minor revisions

• Major revisions

• Reject with resubmission option

• Reject outright

If revisions are invited:

• Address every point methodically, even if you disagree

• Include a point-by-point response letter, quoting each comment and detailing your changes

• Highlight changes in the revised manuscript (tracked changes or coloured text)

• Remain professional and courteous in your tone, even when addressing critical feedback

This stage can significantly improve the quality of your manuscript and is often iterative.

7. After Acceptance: What to Expect

Once accepted:

• The manuscript moves into production for typesetting and proofreading

• You will receive page proofs to check for errors or formatting issues

• Your article will be published online, often ahead of print

Many journals now offer post-publication promotion via social media, email digests, or press releases. Consider sharing your work across your professional networks, institutional website, or platforms like ResearchGate or LinkedIn.

Common Pitfalls to Avoid

• Submitting to the wrong journal or ignoring formatting guidelines

• Incomplete or unclear methods and statistical reporting

• Poor-quality or unlabelled figures and tables

• Failure to respond constructively to reviewer feedback

• Not disclosing conflicts of interest or funding sources

• Overstating findings or making unsupported conclusions

How Medical Writers Can Help

Navigating the journal publication process is not always straightforward — especially when managing clinical workloads, multiple authors, or regulatory expectations. Professional medical writers can support:

• Manuscript drafting and editing

• Journal selection and formatting

• Cover letter preparation

• Literature review integration

• Reviewer response letters

• Compliance with GPP, ICMJE, or CONSORT guidelines

This support can save time, improve manuscript quality, and increase the likelihood of acceptance.

Conclusion

Publishing in a peer-reviewed journal is both an achievement and a contribution to medical progress. By understanding the steps involved and approaching each with clarity, strategy, and attention to detail, you maximise your impact and credibility.

If you need expert support preparing or submitting your manuscript, our medical writing team is here to help.

Contact us today for tailored publication support.