How to Publish a Research Paper: The Complete Guide
Everything researchers need to know to get from completed manuscript to published paper — journal selection, formatting, declarations, peer review, and final submission checks.
Guide
Publishing a research paper involves far more than writing the manuscript itself. From selecting the right journal to formatting declarations, preparing a cover letter, and navigating peer review, each step carries its own set of requirements — and its own failure modes. Studies consistently show that a large proportion of desk rejections result from preventable errors: wrong journal scope, missing declarations, formatting non-compliance. This guide walks through the entire publication workflow in eight stages, with links to dedicated resources for each step so you can go as deep as you need.
The publication process, step by step
Publishing a research paper follows a predictable sequence. Understanding where you are in that sequence — and what comes next — prevents the most common sources of delay and rejection:
Step 1 — Complete your manuscript and run an internal quality check: Before anything else, verify that your manuscript is complete and internally consistent. Run CheckMyManuscript to catch structural gaps, missing sections, and compliance issues before you invest time in submission.
Step 2 — Select your target journal (and two backup journals): Scope fit is the single biggest factor in desk rejection. Identify a primary journal and two backups before you start formatting, so you can pivot quickly if your first choice rejects without review. See our full guide on choosing the right journal.
Step 3 — Prepare all submission components: Most journals require more than the manuscript itself — a cover letter, author contribution statement, conflict of interest declaration, ethics statement, and sometimes suggested reviewers. Prepare these in parallel with manuscript formatting.
Step 4 — Format your manuscript to journal specifications: Each publisher has specific rules for margins, fonts, reference styles, figure resolution, and file formats. Apply the journal's author guidelines or template before submitting. Our manuscript formatting guide covers this in detail.
Step 5 — Submit via the journal's manuscript system: Most journals use ScholarOne, Editorial Manager, or a similar platform. Follow the submission portal's instructions precisely. Upload all required files, complete all metadata fields, and confirm your submission.
Step 6 — Track status and respond to peer review: After submission, monitor the manuscript status in the portal. If the paper passes desk review and enters peer review, you will receive reviewer comments — usually within 4–16 weeks. Responding well to reviewers is its own skill; see our dedicated guide.
Choosing the right journal
Journal selection is the highest-leverage decision in the submission process. A mismatch in scope is the leading cause of desk rejection, often within 24–48 hours of submission. Evaluate every candidate journal on these criteria before committing:
Scope and audience: Does the journal publish papers of this type, topic, and methodology? Read the aims and scope statement, then look at the last 12 months of published articles to verify the match.
Impact factor and reputation: Impact factor measures citation frequency; it is a proxy for prestige and readership, not necessarily quality. Match the journal's standing to your paper's contribution level.
Open access options: Check whether the journal is fully OA, hybrid, or subscription-only. If your funder mandates open access, confirm the journal's compliance and the Article Processing Charge (APC).
Turnaround time: Some journals take 6–18 months from submission to decision; others commit to 30-day first decisions. Check published statistics or community reports if speed matters for your situation.
Acceptance rate: High-prestige journals may have acceptance rates below 10%. Calibrate your expectations and prepare backup journals with a realistic submission strategy.
Indexing: Verify the journal is indexed in the major databases relevant to your field (PubMed, Scopus, Web of Science, ERIC, PsycINFO). Unindexed journals limit discoverability and may not satisfy institutional requirements.
Structuring your manuscript
Most journals in STEM, medicine, and social sciences expect IMRaD structure (Introduction, Methods, Results, and Discussion), often with additional required sections. A complete manuscript includes all of the following:
Title: Specific, informative, and keyword-rich without being a sentence. Avoid unnecessary filler words.
Abstract: A self-contained summary with background, objective, methods, results, and conclusions. Most journals enforce strict word limits (150–300 words). See our full guide on writing a strong abstract.
Keywords: 4–8 terms not already in the title, selected for discoverability in databases.
Introduction: Establishes the research problem, reviews relevant prior work, identifies the gap, and states your specific objective or hypothesis.
Methods: Described in sufficient detail for replication. Includes study design, participants or data sources, instruments, procedures, and analysis approach.
Results: Presents findings without interpretation, supported by tables and figures that are self-explanatory.
Discussion: Interprets results in light of prior work, addresses limitations honestly, and states implications.
Conclusion: A brief synthesis of the main finding and its significance — not a summary of the discussion.
Declarations section: Ethics approval, conflict of interest, funding, data availability, and author contributions (see next section).
References: Formatted to the journal's specified style. Every in-text citation must appear in the reference list and vice versa.
Mandatory declarations every journal requires
Most journals now require a structured declarations section as part of the manuscript itself, separate from the cover letter. Missing or incomplete declarations are a common cause of rejection or revision requests. The standard declarations include:
Ethics statement: Required for any research involving human participants, animals, or identifiable data. State the approving body, approval number, and confirmation of informed consent where applicable.
Conflict of interest (COI): Disclose any financial or non-financial relationships that could influence the research. This includes employment, consultancy, honoraria, stock ownership, and paid expert testimony. 'No conflicts' must also be explicitly stated.
Funding acknowledgment: List all funding sources — grants, institutional support, and any industry funding — with grant numbers where applicable.
Data availability statement: State whether the data underlying the paper are publicly available, restricted, or available on request. Many journals now require a DOI-linked data repository.
Author contributions (CRediT): The Contributor Roles Taxonomy (CRediT) requires listing each author's specific contribution — conceptualization, methodology, writing, funding acquisition, etc. This prevents ghost and guest authorship.
ORCID: Most journals now require or strongly encourage all corresponding authors (and often all co-authors) to provide their ORCID iD. Register at orcid.org if you don't have one.
Formatting for your target journal
Formatting non-compliance is one of the top five reasons manuscripts are returned without review. Before submitting, verify every item in this formatting checklist against the journal's author guidelines:
Reference style: Journals use APA, Vancouver, AMA, Chicago, Harvard, or their own house style. A single incorrectly formatted reference signals that the author guidelines were not read carefully.
File format: Most journals require .docx for the manuscript and accept .pdf as a supplementary format. Check whether figures must be submitted as separate high-resolution files (300+ dpi for print journals).
Word and page limits: Enforce the journal's limits for the abstract, main text, number of figures, and number of tables. These are often strict.
Anonymization for blind review: If the journal uses double-blind peer review, remove all author names, affiliations, and self-identifying references from the main manuscript file.
Line numbering and spacing: Many journals require continuous line numbers and double-spacing to facilitate reviewer annotation.
Supplementary materials: If you are submitting supplementary data, check the journal's format requirements and file size limits separately.
Writing your cover letter
A cover letter is read before your manuscript. A weak cover letter can result in desk rejection before the manuscript is even opened. A strong cover letter makes the editor's job easy. It must include:
Journal fit statement: One to two sentences explaining why this paper belongs in this specific journal, referencing the journal's scope or a recent related article they published.
Summary of the contribution: Two to three sentences stating what you did, what you found, and why it matters — written for an editor who may not be a specialist in your sub-field.
Novelty statement: Explicitly state what is new about this work. Editors look for this.
Confirmation of ethical compliance: One sentence confirming that the research was conducted in accordance with ethical standards and that all required approvals were obtained.
Conflict of interest and prior publication statement: Confirm the manuscript is not under review elsewhere (simultaneous submission is almost universally prohibited), and disclose any prior or related publications.
Suggested reviewers (if invited): Many journals invite 2–4 suggested reviewers. Provide names and email addresses of credible experts in the field who have no conflict of interest with the authors.
Peer review and responding to reviewers
Most journals use single-blind or double-blind peer review, typically with 2–3 external reviewers. After peer review, manuscripts receive one of four decisions:
Accept as is: Rare on first submission. The manuscript is accepted without changes.
Minor revision: Small corrections required — typically factual clarifications, additional citations, or wording changes. Usually a 2–4 week turnaround is expected.
Major revision: Substantial new work required — additional experiments, reanalysis, significant rewriting. The revised manuscript goes back to the same reviewers. This can take several months.
Reject with invitation to resubmit: Distinguishable from outright rejection — the editor sees merit but requires a fundamental restructuring. Treat this as a major revision opportunity.
Reject: The manuscript is not suitable for the journal in its current form. Read the decision letter carefully; editors sometimes provide guidance that helps you redirect to a better-matched journal.
When responding to reviewers, write a structured response letter that addresses every comment point by point, quotes the revised text, and provides a reasoned rebuttal where you disagree. Our full guide on responding to reviewer comments covers this process in detail.
Final pre-submission checklist
In the 24 hours before submitting, run through this checklist. These are the items most likely to trigger an immediate return or rejection:
Verify the manuscript title and abstract exactly match what is in the submission portal metadata fields.
Confirm all authors are listed in the correct order in both the manuscript and the portal, with accurate affiliations and email addresses.
Check that every in-text citation has a corresponding reference list entry and vice versa — no orphan citations, no uncited references.
Confirm all figures and tables are numbered sequentially and cited in the text in order.
Verify the manuscript meets the journal's word limit for abstract and main text.
Confirm the declarations section is complete: ethics, COI, funding, data availability, and author contributions.
Check that all supplementary files are uploaded and referenced in the main text.
For double-blind journals: verify no author-identifying information appears in the manuscript or figure files.
Run a final spell-check and read the abstract aloud — it is what editors read first.
Use CheckMyManuscript to automatically validate journal compliance, catch missing declarations, and identify structural issues before you hit submit.
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Frequently asked questions
The timeline varies significantly by journal and field. From submission to first decision is typically 4–16 weeks. If revisions are required, add another 4–12 weeks per round. Total time from submission to online publication is commonly 6–18 months. Some journals offer accelerated review tracks for an additional fee. Preprint servers allow immediate public sharing while the peer review process is ongoing.
A desk rejection is issued by the editor before the manuscript enters peer review — typically within days of submission. It occurs when the manuscript falls outside the journal's scope, fails to meet basic formatting requirements, has obvious methodological flaws, or lacks novelty for that venue. A peer review rejection comes after external experts have evaluated the manuscript in detail. Desk rejections are faster and leave you free to resubmit immediately elsewhere; peer review rejections usually include substantive feedback that can strengthen the manuscript.
Start with scope fit: read the journal's aims and scope and browse recent issues to verify that papers like yours are published there. Then consider impact factor and prestige relative to your paper's contribution, open access requirements from your funder, and turnaround time if speed matters. Always prepare two backup journals before you submit, so you can redirect quickly if the first choice rejects without review.
Most journals require: an ethics statement (for research involving human or animal subjects), a conflict of interest disclosure, a funding acknowledgment with grant numbers, a data availability statement, and an author contributions statement (CRediT taxonomy). Many also require ORCID iDs for all authors. Missing or incomplete declarations are a common cause of revision requests and occasionally desk rejection.
Yes, in most cases. The majority of journals — including those published by Elsevier, Springer Nature, Wiley, and PLOS — explicitly permit preprint posting before or during peer review. Check the journal's preprint policy before posting. A small number of journals, particularly in clinical medicine, restrict prior public disclosure. Preprint servers such as arXiv, bioRxiv, and SSRN are widely used for this purpose.
Scope mismatch is the leading cause of desk rejection — the manuscript addresses a topic or uses a methodology outside what the journal publishes. After scope, the most common reasons are insufficient novelty for the venue, methodological weaknesses, and incomplete or missing declarations. For papers that pass desk review, insufficient engagement with prior literature and overclaiming in the discussion are the most frequent peer review criticisms.