Publishing research isn’t just the final step of a project—it’s what gives your work power. A well-prepared manuscript not only earns you academic recognition; it can also influence future research priorities, clinical guidelines, and even national policies. But the journey from completed study to published paper is often more complex than it first appears.

Many researchers, whether early-career or well-established, struggle with the same concerns. Have I formatted this correctly? Will it be rejected outright? Does the journal’s scope align with my goals? These questions are valid, and the stakes are high.

In this article, we’ll guide you through the essential steps to publish a scientific manuscript, sharing practical tips for publishing a research paper and helping you navigate the often-overlooked but crucial process of preparing a research manuscript for submission. From choosing the right journal to avoiding common pitfalls, you’ll learn how to position your paper for the best chance of acceptance.

 Understand the Manuscript Submission Process

Preparing a research manuscript for submission isn’t just about writing—it’s about aligning your work with the broader research publication workflow. Understanding the process from start to finish can help you make strategic decisions that improve your chances of success and reduce delays.

From Research to Publication: The Key Stages

The journey from research to publication typically follows several key steps. After completing your study and analysing the results, you’ll draft your manuscript according to the target journal’s guidelines. Then comes submission, followed by peer review, revisions, acceptance, and finally, publication. Each of these stages plays a critical role in ensuring the quality and integrity of academic work.

Knowing where you are in this workflow—and what’s expected next—can help you prepare thoroughly and avoid common pitfalls.

Choosing the Right Journal for Your Manuscript

Selecting a suitable peer-reviewed journal is one of the most important decisions in the research publication workflow. A mismatch can lead to delays or outright rejection, even if your research is sound. Consider the journal’s scope, readership, recent articles, and turnaround times. Importantly, don’t overlook impact factor considerations or whether the journal offers open access vs traditional publishing options.

If you’re unsure where to start, check out our guide to journal selection—it’s packed with tips and tools to help you assess the credibility and fit of potential journals.

What Publishers Look For in a Submission

Editors and reviewers want to see that your work is not only scientifically sound but also clearly presented, relevant, and well-structured. A good manuscript demonstrates novelty, significance, and adherence to ethical standards. Publishers also appreciate submissions that follow formatting instructions precisely—this shows attention to detail and respect for the journal’s process.

Structure and Components of a Scientific Manuscript

Understanding the structure of a scientific manuscript is essential for effective communication and successful publication. Journals expect a clear, logical format that highlights your study’s relevance, methodology, and outcomes. Whether you're a first-time author or an experienced researcher, knowing how to write a scientific manuscript that aligns with journal standards is a core part of manuscript preparation in medical research.

Title and Abstract

The title and abstract are arguably the most important parts of your manuscript. They’re the first (and sometimes only) sections a reader or reviewer will see—so clarity, precision, and relevance are key.

Your title should concisely reflect the key findings and subject matter of your research. It’s estimated that readers spend less than two seconds deciding whether a paper is worth exploring further, so make that moment count. A well-crafted title often includes keywords related to your specialty, the specific disease or condition studied, and the intervention or methodology used. This not only boosts discoverability but also immediately signals the paper’s relevance to its intended audience.

When it comes to the abstract, journal-specific word limits are common, so check the requirements carefully. A structured abstract—divided into sections like background, methods, results, and conclusions—can greatly improve readability, unless the journal explicitly prefers an unstructured format. Your abstract should clearly convey the study’s purpose, main findings, and significance, offering a compelling summary that encourages further reading.

Introduction

The introduction sets the tone for your entire manuscript. It should be focused and concise, offering just enough background to establish context and demonstrate the relevance of your research. A useful format to follow is problem–gap–hook: describe the problem your study addresses, outline the specific gap in the existing literature, and state your study’s objective in addressing that gap.

Methods and Materials

This section is critical for transparency and reproducibility. It should clearly outline how the study was conducted and enable others to replicate the work if needed. Use past tense throughout.

Key elements to include:

• Study design: Specify if the study is prospective or retrospective, interventional or observational, cohort, randomised controlled, or case-control.
• Setting and duration: Where and when the study took place.
• Participants: Inclusion and exclusion criteria, recruitment process, and informed consent.
• Ethical approval: Include the name of the reviewing body and approval number, if applicable.
• Procedures and protocol: Describe what was done, referring to existing protocols or supplementary materials if appropriate (e.g. for lab techniques like PCR, specify the type but not every step).
• Drugs and equipment: Use both generic and brand names, include the manufacturer and location.
• Statistical analysis: State the type of analysis used and any software packages applied.

Results

This section presents your findings clearly and objectively, without interpretation. Focus on:

• Participant flow and baseline characteristics
• Primary and secondary outcomes
• Any prespecified subgroup analyses or exploratory findings

Use tables and figures strategically to support your narrative—don’t repeat the same data in multiple places.

Discussion

Your discussion interprets the results, connects them to existing literature, and highlights your study’s contributions. Start with a lead paragraph summarising the key findings, then move into interpretation.

A strong discussion also:

• Acknowledges limitations and potential biases
• Pre-empts likely reviewer criticisms
• Explains how your findings support or challenge existing knowledge

Conclusion

This should be short and punchy. Summarise the main take-home points of the study in 2–4 sentences. Avoid overstating the significance of your results—clarity and accuracy matter more than dramatic claims.

References

Ensure your references are formatted according to the journal’s style guide. Use a reference manager to stay consistent and save time during revisions. Most journals require references to be up-to-date, relevant, and peer-reviewed.

Figures, Tables, and Supplementary Materials

Include only those visuals that are essential for understanding the data. Each figure or table should:

• Be high-quality and easy to interpret
• Stand alone, with clear and concise captions
• Avoid redundancy—don’t restate in text what’s already clear in visuals

Consider how figures will appear in grayscale, as not all journals print in colour.

Formatting Your Manuscript for Publication

Formatting a manuscript for publication may feel like a technicality, but it’s often the first hurdle between you and a successful submission. Even high-quality research can be delayed or rejected for failing to follow a journal’s specific requirements. As part of knowing how to prepare a manuscript for publication, attention to detail here can save you time, stress, and unnecessary rounds of revision.

Following Journal Guidelines to the Letter

Every journal has its own set of research manuscript guidelines, and these can change over time. It’s essential to check the journal’s author instructions not just when you start writing, but again before submission to make sure nothing has been updated. This includes requirements for:

• Manuscript length and structure
• Referencing style
• File formats
• Blinded documents (for double-blind peer review)
• Submissions of figures and tables as separate files, including resolution and format

Also, don’t overlook the journal submission requirements for authorship. Many journals follow ICMJE or similar criteria, which outline who qualifies as an author and how contributions should be reported. Failure to comply here can raise ethical red flags or delay acceptance.

Common Formatting Pitfalls to Avoid

Some of the most common mistakes we see when formatting a manuscript for publication include:

• Submitting figures or tables in the wrong format or resolution
• Including author names on blinded documents
• Inconsistent or incorrect referencing
• Using non-standard abbreviations without defining them
• Failing to follow word count or character limits for sections like the abstract or title

These issues might seem small, but they can lead to desk rejection or long delays in peer review.

Writing Tips for Clarity and Impact

Strong, clear writing is just as important as robust data when it comes to getting published. Reviewers and editors read dozens of papers a week, so the more accessible and compelling your manuscript is, the more likely it is to stand out. These best practices for academic writing will help you refine your message and improve readability, ultimately increasing your chances of publication.

Using Clear, Concise, and Objective Language

One of the most common challenges in manuscript writing for researchers is the tendency to overcomplicate. Aim for clarity over cleverness. Use precise language, avoid jargon when possible, and remove unnecessary words. Each sentence should serve a purpose—supporting your argument, clarifying your findings, or guiding the reader logically through the paper.

When writing and editing a scientific paper, objectivity is key. Avoid overstating your results or using overly promotional language. Stick to the evidence and let the data speak for itself. Use active voice where possible, and ensure tense usage is consistent (e.g., past tense for methods and results, present tense for established facts).

Tailoring Your Manuscript to Your Audience

Remember: your audience is more than just your peers. Reviewers, editors, and even multidisciplinary researchers may read your paper. Think about their expectations and familiarity with the subject. Tailor your tone, terminology, and level of background detail accordingly.

For highly specialised journals, a more technical style is appropriate. For broader publications, your manuscript should be accessible to readers outside your immediate field. This is especially important when discussing clinical relevance or broader implications of your findings.

The Role of Medical Writers and Editors

Manuscript writing isn’t easy. Even if you enjoy writing, it’s time-consuming and often stressful, especially given that getting your research published is vitally important to you. 

This is where medical writers and editors can help. A good medical writer, with expertise in your speciality, will be able to communicate your research with clarity, accuracy and a compelling narrative. In other words, they know (because they’ve done it many times before) exactly how to write and format a manuscript to maximise its chances of publication.

Of course, not all medical writers are equal. If you’re thinking about using one, it’s important to make sure they have the experience you need, not just of writing, but ideally of research in your subject area. Rx Communications writers all have research and clinical experience, and we match every project to a writer with specialist knowledge. 

Review, Review, Review

No matter how well-structured or insightful your manuscript is, it can almost always be improved with careful review, and more than once. After your first draft, build in time for multiple rounds of editing. Step away from the paper for a day or two, then come back to it with fresh eyes. This helps you catch inconsistencies, unclear phrasing, or logical gaps that might not have been obvious while writing.

One of the best ways to strengthen your manuscript is to ask a colleague—ideally someone not directly involved in the study—to review it. They can offer a more objective perspective and point out areas that are confusing or underdeveloped. What seems clear in your head may not be clear on the page, especially for readers outside your immediate research team.

Our team often helps researchers at this stage by providing an external review, focusing on clarity, coherence, and readability, to ensure the final version is polished and publication-ready. Whether it’s a peer, a mentor, or a professional editor, getting that extra layer of feedback can make all the difference. The goal is a manuscript that is not only scientifically sound but also easy to read, understand, and evaluate.

Preparing for Submission

After all the planning, writing, and revising, you’re nearly at the finish line—but don’t rush the manuscript submission process. Taking time to do a few final checks, prepare a strong cover letter, and understand what happens after you hit "submit" can help you avoid unnecessary delays and improve your chances of acceptance.

Final Checks Before Submission

Before submitting, go through a thorough manuscript submission checklist, which you can find at the end of this article.

Creating a Strong Cover Letter

The cover letter for journal submission is your opportunity to briefly introduce your study, explain its relevance, and highlight why it’s a good fit for the journal. Keep it concise (usually one page), and include:

• The manuscript title and type of article
• A brief overview of the research question and main findings
• Why the research is important or novel
• Why this journal is the appropriate venue for the work
• A statement that the manuscript has not been submitted elsewhere

What to Expect After Submission

Once submitted, your manuscript enters the journal’s editorial workflow. Here’s what typically happens next:

1. Initial screening: The editor checks for fit, scope, and formatting.
2. Peer review: If it passes initial screening, your manuscript is sent out for review, which can take several weeks to months.
3. Decision letter: You’ll receive a decision—acceptance, minor or major revisions and resubmissions, or rejection.

If revisions are requested, take reviewer comments seriously and respond to each point clearly and respectfully. 

Understanding how to submit a research paper to a journal and what happens afterwards can make this final phase feel less daunting, and bring you one step closer to publication success.

Common Reasons for Rejection—And How to Avoid Them

Manuscript rejection is a common part of the publishing process, even for experienced researchers. Understanding the common reasons for manuscript rejection can help you avoid setbacks and improve your chances of success.

Some rejections happen early—desk rejections occur before peer review, often due to a poor fit with the journal’s scope, failure to follow submission guidelines, or a weak abstract. Others come after peer review, where technical flaws (e.g. small sample size, inadequate methods) or editorial issues (e.g. unclear writing, lack of novelty) are flagged by reviewers.

Take reviewer comments seriously. Even if your manuscript is rejected, their feedback can guide you toward a stronger resubmission elsewhere. Addressing technical gaps, tightening your writing, or reframing the study’s significance can make a major difference.

For a more detailed look at these issues—and practical tips on what to do next—see our articles on what to do when your manuscript is rejected and the common reasons for manuscript rejection.

Final Thoughts: Setting Yourself Up for Success

Publishing your research is one of the most rewarding parts of the scientific process, but it takes more than just good data. From choosing the right journal and following formatting requirements to writing with clarity and anticipating reviewer expectations, every step matters.

Thorough preparation is key. By understanding the manuscript structure, aligning with journal submission requirements, and reviewing your work with fresh eyes (and ideally, external feedback), you give your manuscript the best possible chance of success. Starting early also helps, especially when coordinating co-authors, collecting disclosures, and crafting a strong cover letter.

Whether you’re preparing your first submission or your fiftieth, approaching the process strategically will always serve you well. With the right mindset, tools, and support, you’ll be well on your way to turning your research into a publication that makes an impact.

Ready to Submit? Don’t Miss a Step

Before you hit “submit,” make sure everything is in place with our free Journal Submission Checklist—a practical, easy-to-follow resource designed to help you stay organised and confident throughout the manuscript submission process.