Handling manuscript submission, revision and acceptance: a young author’s guide

INTRODUCTION

Publishing a research work in a reputable journal is a dream of every researcher. The publication process is quite demanding and requires sheer patience and persistent efforts; it offers valuable rewards, including academic credibility, professional growth, and wider recognition within research community.¹ Rate of rejection among different indexed journals is varied between 80 and 85% even some journals have reported it to be around 90-95%.² Many successful publications have undergone one/more rejections before eventual acceptance.

Rejection is not a sin

An average time spent for quality research is months, sometimes years, designing and carrying out their work, followed by long hours drafting and refining the manuscript. Then comes the anxious waiting period when the editorial decision finally arrives, rejection often brings frustration and discouragement. In fact, many scholars begin to see rejection as fate and stop writing their next manuscript. We should not forget the history that more than 20 Nobel laureates had their articles initially rejected by many journals. It is rare to get the go-ahead without any changes in manuscript.³

We strongly feel that; a good-quality research paper will find the space it deserves in top-tier journals. Interestingly, it is reported that 62% of papers have been rejected at least once by other journals before getting published.⁴ An author should reflect on how their work benefits them and what they can learn from it. Keeping the target audience in mind also helps in selecting the most appropriate journal for publication or the best platform to present the work. Ultimately, publishing scientific work demands perseverance, patience, and sustained effort. However, the sense of achievement that comes with acceptance and the contribution your work makes to the scientific community make the journey worthwhile. Rejection is a routine part of academic publishing and success in publishing is rarely accidental it grows from preparation, clarity of purpose, and continuous learning

AIM

Rejection in academic publishing is a common experience, yet it is not openly talked about, and guidance on handling it is often limited. Many authors are left to cope with disappointment on their own. The existing gap highlights the need for a practical guide to support young researchers in strengthening their work. Recognizing their issues can help scholars improve quality and achieve publication success. This article explores the typical reasons why manuscripts are declined and offers practical suggestions to help researchers respond constructively and move forward with confidence.

Novice in the study

This study identifies common reasons papers are rejected, rather than concentrating only on responding to reviewers or improving writing style, it brings together theory, methodology, and structure into one cohesive framework. It offers practical guidance to help researchers and importantly, it encourages young authors to strengthen their manuscripts from beginning, promoting thoughtful preparation instead of last-minute corrections after peer review.

PHASE OF MANUSCRIPT PUBLICATION

Selection of right journal before finalizing manuscript

Choosing a suitable journal is one of the most effective ways to avoid desk rejection. Even a well-written and strongly written study can be rejected early if it does not fit the journal’s scope. To improve their chances, authors should carefully review the journal’s aims and scope, look through previously published articles, and ensure that their manuscript aligns with the interests and expectations of the journal’s audience. Well-known journals receive a high volume of submissions. Here are some points to be remember to select a journal.⁵

Assess the journal’s quality

Check the impact factor

Review the journal’s impact factor to understand its academic influence and visibility within the field.

Verify legitimacy

Ensure the journal’s authenticity, ethical, and maintains high publication standards. Avoid predatory journals that may appear credible but lack proper peer review.

Use trusted resources

Websites such as Think. Check. Submit. developed by academic publishers and scholarly associations can help you evaluate whether a journal is reliable and appropriate for your work.

Understand the journal’s scope

Look for aims and scope

Carefully read the journal’s aims and scope section. Most scholarly journals focus on specific topics within a broader discipline.

Match your research topic

Ensure that your manuscript aligns closely with the journal’s subject focus to improve the likelihood of acceptance.

Consider the peer-review timeline

Since the peer-review process may take several months, choosing the right journal at the beginning helps avoid delays and repeated submissions.

Follow author guidelines carefully

Most academic journals provide clear guidelines that act like a roadmap for authors. These instructions explain how to structure the paper, including formatting the title page, placing tables and figures, following the required reference style, and staying within the specified word limit.

Read instructions before writing

Always review the journal’s instructions for authors before preparing your manuscript.

Adhere to submission requirements

Pay close attention to formatting style, word limits, referencing style, structure, and submission procedures.

THE JOURNAL PROCESS FROM DESK REVIEW TO ACCEPTANCE

Writing a manuscript

Good, precise writing is like an art and skill that is important for emerging authors. In most healthcare education systems around the world, the art of writing a manuscript and knowledge of the path to publication is rarely taught.

A strong manuscript rests on two pillars: Meaningful content and effective presentation. While exploring new or trending topics can boost publication chances, genuine interest in the subject matters is just as important because it’s passion that keeps you going through the toughest stages of research. Strong command of English and grammar is essential for publication, so invest time to adhere strictly to scientific writing principles.⁶

Before we move ahead, let us briefly highlight a few key takeaways.

Ready to rewrite

Strong papers are rarely written in one sitting. Revise your work again and again even experienced scholars do. Remember, you are writing for readers, so clarity should always come before personal preference.

Write and refine step by step

Use simple language, remove repetition, and ensure smooth connections between sections. Check grammar and flow carefully. Ask colleagues to review your draft. Never submit without a thorough final review.

Ask for colleague’s feedback

Share your work with co-authors, mentors, and peers. Early criticism may feel uncomfortable, but it helps refine arguments and improve quality.

Treat writing as a skill to master

Producing an outstanding paper is not luck it is practice, patience, and persistence. With consistent effort and thoughtful refinement, excellence in academic writing becomes achievable.

How to choose title

A paper’s title is the first thing readers notice when scanning a journal or database, so it plays a key role in attracting attention. The title should be clear, concise, and clearly reflect the aim of study without being confuse. Important keywords that make it easier for readers to find the article are used in an effective title, ideally at the start. It shouldn't be excessively lengthy, unclear/imaginative, but rather precise, educational, and captivating.

Writing the abstract

The abstract is usually the most read section of a scientific paper, and in many cases, it may be the only part that readers go through. After the title, it is usually the first section readers examine, and sometimes it is the only part they access. For this reason, it must clearly and accurately summarize the entire study. Research objective should be clearly stated and separated from general background information. Methods should outline study design and essential procedures without too much detail. Results must highlight only the most important findings, and conclusion should directly reflect what is presented in paper. Authors should follow journal’s guidelines regarding structured/unstructured formats. Avoid unnecessary abbreviations and never include references.⁷

Introduction/background part

The introduction of a scientific article is like the opening scene of a movie. It captures attention and gives readers an idea of what to expect in the rest of the paper. A well-written introduction should be clear, engaging, and logically organized. It begins with a brief overview of the topic based on current literature, helping readers understand the background. Next, it narrows down to the specific problem being addressed and highlights key references related to the issue. Finally, it clearly states the purpose or objective of the study. An unorganised introduction may discourage readers, even if the research itself is strong and valuable.²

Methods

The methodology section of paper explains exactly how the study was conducted and allows readers to judge its reliability. Weak or unclear methodology is a common reason for manuscript rejection. This section should be written in the past tense and provide enough detail for others to understand or replicate the work. It should begin by explaining the whole study design, such as a case-control study, cohort study, or clinical trial describe how participants were selected, how the sample size was determined, and whether statistical power calculations were performed. Quality control steps, and blinding methods must be explained to demonstrate scientific rigor. Ethical approval and informed consent statements are essential.

Results

The results section should follow the same logical order as the methods section and be written in the past tense. Only findings related to the research objectives need to be reported. Authors need to avoid presenting unnecessary data that do not contribute to answering the main research question. Tables and figures should be used to improve clarity, and repetition between text and visuals should be minimized. Primary outcomes must be presented before secondary findings. Both statistically significant and non-significant results should be reported to maintain transparency. Descriptive statistics, confidence intervals, and exact p values should be provided where appropriate. Any missing data, unexpected outcomes, or deviations from the original plan should be explained honestly. No interpretation or conclusions should appear in this section, as that belongs in the discussion section.⁹

Discussion

A well written discussion is essential because it explain readers of the key findings and clearly explains how the study adds meaningful value to the field. The discussion section interprets the findings and explains their importance. It should begin with a brief summary of the main results in relation to the study objectives. Authors must then compare their findings with similar research, highlighting similarities, differences, or new contributions. This section should answer two key questions: why are these findings important, and who benefits from this knowledge? Only the most relevant data should be referenced, and no new results should be introduced. The discussion should focus on meaning and interpretation rather than the repeating numerical results.¹⁰

Conclusion

The ending must be clear, concise, and directly supported by the study findings. Authors should avoid exaggerating results or making claims beyond the evidence. A strong conclusion reinforces the main message of the research and explains its significance.

A cover letter

The cover letter to journal reflects your professionalism, during manuscript submission. Writing a clear, polite, and respectful letter to the editor shows that you value the journal and the peer review process. It should briefly explain the importance of your study and confirm that the work is original. A strong cover letter explains the relevance of the manuscript to the journal’s audience and highlights its key findings and significance. It should mention any related submissions, prior communication with the editor, and confirm exclusive submission. Address the editor by name, include the title, article type, and study summary. Conclude with author details, ethical compliance, and a statement confirming all authors’ approval and originality of the work.¹¹

AFTER SUBMISSION PROCESS

The first hurdle: understanding desk rejection

Once submitted, the manuscript is evaluated by the editor-in-chief, often in consultation with the editorial team. Editors initially look at the title and the subject on which the research has been based. When it is not of much interest to the readership, the paper can be directly rejected at the level of desk assessment. A considerable proportion of submissions may be declined at this preliminary stage, without external peer review. Such decisions are sometimes based on concerns about manuscript quality, overall presentation of content but more commonly on lack of alignment with the journal’s focus. Ethical concerns such as authorship disputes, undeclared conflicts of interest, missing ethical approval, or lack of informed consent can also lead to rejection. Editors often choose to provide a prompt decision so authors can seek a more suitable outlet without prolonged waiting. Thus, they reject the manuscript even without sending it to the reviewer or may send it only to one reviewer to confirm the decision.⁵

Peer review process

Manuscripts that proceed to peer review compete with other submissions under consideration. Only those that meet high standards in originality, clarity, and scientific rigor are likely to progress toward acceptance. Manuscript that stands out among others is one that gets accepted, while rest may be rejected with feedback explaining reasons in reviewers’ comments.

It rarely happens that a ‘stand out’ manuscript is accepted without any improvements. Often for such articles reviewer will ask authors (through editor-in-chief) to improve upon points listed to make it even more apposite and worthy of being published.

Accept without changes

This outcome is exceptionally rare. It indicates that the manuscript meets all editorial and reviewer expectations and can proceed directly to publication without any alterations.

Conditional acceptance pending major revision

Here, the journal sees potential but requires substantial improvements. After the authors revise the manuscript, it is often reassessed sometimes by the original reviewers. Although acceptance is not guaranteed, the probability improves compared to the initial submission.

Conditional acceptance with minor revision

Only minimum changes, such as clarifications or formatting corrections, are requested. Once these are satisfactorily completed, publication usually follows

MANUSCRIPT REJECTED! TURNING REJECTIONS INTO ACCEPTANCE

It is really disheartening when your paper gets rejected even after two three revisions and positive reviewer’s comments. Authors work very hard to conduct research and one should not get disappointed by rejections. Most top journals have almost 80% rejection rates. If you wish to publish good-quality articles and have taken rejections, positively.¹²

In 2009, the Indian Journal of Dermatology, Venereology and Leprology (IJDVL) received 655 submissions, of which 28% were accepted and 66% rejected, the most common reasons for rejection included weak study design, inadequate methodology, small sample sizes, flawed analysis, and unclear writing, along with issues such as lack of novelty, ethical concerns, plagiarism, and unsupported conclusions, while the growing number of submissions coupled with a lower acceptance rate reflects increasingly stringent peer review standards.¹³

Here we need to remember that don’t the readers deserve the best of the best research for updating their knowledge? Do they deserve the same old findings well established several times in the literature? The answer is certainly ‘No’!

One must remember that world’s best revolutionary trials and path breaking research are submitted to these prestigious journals; hence, a paper of a lower quality and priority is most likely to be rejected for saving reputation of journals. Rejection is a common part of academic publishing and should not be viewed as a personal failure. Editorial decisions are based on established criteria, journal priorities, and competitive standards. Authors should carefully review feedback, reflect objectively on the manuscript, and identify areas for improvement. Constructive criticism offers an opportunity to strengthen both the research and its presentation.

REVISION AFTER PEER REVIEW

Major revisions require substantial time and effort; consider carefully whether to proceed or submit to another journal. Respond to every reviewer comment point by point, even if it seems unclear or incorrect. Prepare a detailed response letter listing each comment followed by your explanation or revision. Clearly highlight all changes made in the revised manuscript. If you disagree with a comment, explain your reasoning respectfully and justify your decision. Do not rush the revision or ignore any feedback. Maintain a professional and courteous tone at all times. Multiple rounds of revision are common in academic publishing.

Appeal the decision

If the reviews seem clearly unfair, you may write to the editor requesting reconsideration. Appeals are rarely successful and require strong justification.

Submit to another journal

Revise the manuscript by incorporating previous feedback to strengthen it before resubmission elsewhere.

Discontinue the article

If major methodological or data flaws compromise the study’s validity, it may be appropriate to reconsider or abandon the submission.

PLAGIARISM CONTROL

Plagiarism in academic world is viewed as unethical and a form of academic dishonesty. Although it is not a direct criminal act, it can violate copyright laws, and in academic and professional settings it is taken seriously, often leading to actions such as penalties, suspension, or even removal by institutions or publishers.

Authors must present original work and properly credit all sources. Using others’ ideas, words, or data without acknowledgment, artificial intelligence apps use, even after slight rewording, is unethical. Submitting similar or overlapping work to multiple journals without disclosure is also misconduct. Such practices damage credibility and may lead to rejection or penalties. With advanced plagiarism detection tools now widely used by journals, maintaining honesty, transparency, and proper citation is essential for responsible and ethical scientific publishing.¹⁴

Always give proper credit to the original sources, add acknowledgments, use footnotes and quotation marks when needed, take permission for long quotations, remember that common facts do not need citation, and avoid self-plagiarism by getting permission before reusing your own published work.

Accurate referencing is essential in medical writing, as it ensures proper credit and strengthens credibility. Incorrect or missing citations can raise concerns about quality, honesty, or even plagiarism.

Once the article is accepted the manuscript then undergoes copyediting to improve clarity and overall quality, followed by formatting. You will receive a PDF proof, often with editorial queries such as missing references, unclear statements, or incomplete authors details. This stage is your final opportunity to correct errors, spelling mistakes or adding missing information. Here no scope to change, edit the content.

DISCUSSION

It is important to understand that editors do not reject papers lightly. Their responsibility is to ensure that readers receive the most meaningful, current, and impactful research. And honestly, they deserve nothing less than the very best.

When your manuscript gets rejected, the most important thing is to pause and stay composed. It’s natural to feel disappointed, but replying in frustration or sending an emotional appeal rarely helps. In most cases, journals do not reopen discussions once a decision is made. Take time to carefully read the reviewer’s comments and understand the real reasons behind the rejection. Sometimes the issue lies in the quality of the work at other times, the manuscript simply does not align well with the journal’s scope.

If the study is solid but not a good fit, consider submitting it to a more suitable journal. Occasionally, editors themselves may suggest or arrange a transfer to another journal where the paper stands a better chance.^15,16

If possible, continue the work and resubmit when it is more robust. Before trying again, invest time in carefully studying the aims, scope, and expectations of your next target journal to improve your chances of success.

Journal decisions usually fall into three categories: acceptance, revision, or rejection, and these may occur with or without peer review. When revisions are requested, authors must respond to every comment carefully and respectfully, even if they disagree with the reviewers’ suggestions. Always communicate with the editor in a respectful and professional manner.

If your manuscript is rejected, do not feel discouraged. Carefully review the feedback, learn from the comments, and consider submitting the revised work to another suitable journal or reflect on whether further improvement is needed before resubmission.

CONCLUSION

Careful planning before initiating a paper is essential. High-quality research paired with clear, well-structured writing eventually find a suitable platform. Rather than focusing on quantity of publications, researchers should prioritize depth, rigor, and originality. Allowing adequate time for thoughtful revision and continuous refinement increases the likelihood of eventual success. Scientific publishing is competitive and demanding, but persistence, careful preparation, and dedication to excellence ultimately lead to rewarding outcomes.

Funding: No funding sources

Conflict of interest: None declared

Ethical approval: Not required

REFERENCES

1. 1. Kara-Junior N. Why, what, and where to publish scientific research. Arq Bras Oftalmol. 2024;88(1):e20241013.
2. 2. Hall SA, Wilcox AJ. The fate of epidemiologic manuscripts: a study of papers submitted to Epidemiology. Epidemiology. 2007;18(2):262-5.
3. 3. Campanario JM. Rejecting and resisting Nobel class discoveries: accounts by Nobel Laureates. Scientometrics. 2009;549-65.
4. 4. Khadilkar SS. Rejection blues: why do research papers get rejected? J Obstet Gynaecol India. 2018;68(4):239-41.
5. 5. Shah J, Smart P. An author's guide to submission, revision and rejection. Ann R Coll Surg Engl. 2015;97(8):546-8.
6. 6. Sackett DL, Richardson WS, Rosenberg W, Haynes RB. How to practice and teach evidence-based medicine, 2^nd ed. Edinburgh: Churchill Livingstone. 1997.
7. 7. Rane NL, Choudhary S, Rane J. Publishing academic books in emerging fields: strategies for success and overcoming challenges. In: How to publish academic books: a guide to publishing monographs, edited volumes, textbooks, and theses. Deep Science Publishing. 2024;145-89.
8. 8. Andrade C. How to write a good abstract for a scientific paper or conference presentation. Indian J Psychiatry. 2011;53(2):172-5.
9. 9. Hunter MK, Russell AJ, Maldonado G, Burstyn I. Exploring the proper use of p-values and confidence intervals in leading epidemiology journals. Glob Epidemiol. 2026;11:100247.
10. 10. Aga SS, Nissar S. Essential guide to manuscript writing for academic dummies: an editor's perspective. Biochem Res Int. 2022;2022:1492058.
11. 11. Kumar M. Handle with care: authorship challenges and conflicts in research publication. Int J Community Med Public Health. 2024;11(12):5057-63.
12. 12. Nicholas D. How to choose a journal and write a cover letter. Saudi J Anaesth. 2019;13(1):S35-41.
13. 13. Sullivan GM. What to do when your paper is rejected. J Grad Med Educ. 2015;7(1):1-3.
14. 14. Dogra S. Why your manuscript was rejected and how to prevent it? Indian J Dermatol Venereol Leprol. 2011;77(1):123-7.
15. 15. University of Oxford. Plagiarism. Oxford: University of Oxford. Available at: https://www.ox.ac.uk/students/academic/guidance/skills/plagiarism. Accessed on 06 May 2026.
16. 16. Norman G. Data dredging, salami-slicing, and other successful tips to ensure rejection: twelve tips on how to not get your paper published. Adv Health Sci Educ Theory Pract. 2014;19(1):1-5.