Journal submission: a complete guide for researchers

Submitting a manuscript to a journal is rarely the straightforward step it appears on paper. Between choosing the right venue, formatting your work to the letter of the author guidelines, writing a cover letter that earns a second look, and navigating the submission system itself, there are a dozen points where a promising paper can stall — or land on the desk-reject pile without ever reaching a reviewer.

This guide walks you through the full process: from the moment you decide a manuscript is ready to the moment the editor’s decision lands in your inbox. It is written for researchers who have done the science and written the paper, and now need to get it published.

If you are still deciding where to submit, start with our guide to journal selection first.

The end-to-end submission workflow

Step 1: confirm scope and fit

Before opening the submission portal, re-read the journal’s aims and scope with fresh eyes. Ask whether your study design, methodology, sample size, and topic genuinely align — not just tangentially. Editors desk-reject a significant portion of submissions for scope mismatch, and no amount of polish recovers from that. Check recent issues to see what the journal has published in the past twelve months; editorial appetite shifts.

Also verify the journal’s standing. Confirm it is indexed in the databases relevant to your field (PubMed, Scopus, Web of Science, etc.) and is not on any predatory publisher watchlists. Our journal selection guide covers this in more depth.

Step 2: read the author guidelines — twice

Every journal publishes detailed author instructions. Read them in full before you touch the manuscript. The specifics vary widely:

• Word limits — often separate limits apply to the abstract, main text, and reference list
• Structural requirements — some journals require a structured abstract (Background / Methods / Results / Conclusions); others prefer a single unstructured paragraph
• Reference style — Vancouver, APA, AMA, or a journal-specific variant; check whether references should be numbered in order of citation or alphabetized
• Figure and table formatting — file type, resolution (typically 300 dpi for print), and whether legends go in the main text or a separate file
• Supplementary materials policy — what can be submitted as a supplement versus what must appear in the main body
• Blinding requirements — double-blind journals require that author names and affiliations be removed from the manuscript file itself, not just the submission form

Return to the guidelines after you have prepared your submission package. A second read catches the things you missed when the task felt abstract.

Step 3: prepare the submission package

A complete submission typically includes:

1. Title page — full title, all authors with affiliations, corresponding author contact details, word count, and any trial registration numbers
2. Manuscript file — the paper itself, blinded if required
3. Abstract — standalone and self-contained; many readers will see only this
4. Keywords — follow the journal’s guidance on number and controlled vocabulary (MeSH terms for biomedical journals, for example)
5. Cover letter — addressed to the editor; see the full section below
6. Declarations — ethics approval, informed consent, data availability, conflicts of interest, funding sources, author contributions (CRediT taxonomy is increasingly standard)
7. Figures and tables — as separate high-resolution files, plus their legends
8. Supplementary files — labelled clearly and referenced in the main text
9. Suggested and excluded reviewers — many portals make this optional but it is worth completing thoughtfully

Before you upload anything, run a thorough pre-submission review of the manuscript. Editors and reviewers form rapid impressions; clarity, internal consistency, and freedom from careless errors all signal that the underlying work is careful too. Start a free review on PerfectPaper to get substantive AI feedback on argument structure, methods reporting, and prose before you submit.

Step 4: navigate the submission system

Most journals use Editorial Manager, ScholarOne (Manuscript Central), or a publisher-built portal. Have your ORCID iD ready — it is required or strongly recommended by most systems. Upload files in the order the system specifies; it usually generates a PDF proof for you to check. Review that proof carefully: figures can reflow, equations can break, and special characters can corrupt in the conversion. Approve only when satisfied.

Record the submission confirmation number and date. You will need it for any correspondence and for tracking the manuscript’s progress.

How to write a strong cover letter

The cover letter is not a formality. Editors read them, and a well-written one provides context the manuscript cannot supply on its own: why this journal, why now, and what the paper contributes that distinguishes it from prior work.

What to include

• Opening — the full title, the journal name (match exactly), and the submission type (original article, brief communication, etc.)
• The central finding and its significance — two to four sentences summarising what you found and why it matters to the journal’s readership; write this as you would explain it to a thoughtful colleague in an adjacent field
• Fit to the journal — one sentence making the connection explicit; cite a recent paper in that journal if there is a genuine intellectual link
• Declarations of uniqueness — confirm the work has not been published elsewhere, is not under consideration at another journal, and does not duplicate your own prior work
• Any editorial requests — if the journal requires you to identify suggested or excluded reviewers, you can note this here or complete it in the portal form
• Conflicts of interest — brief statement even if the answer is “none”
• Corresponding author contact — name, institutional email, phone (some journals require it)

Cover letter template

Dear [Editor-in-Chief name] / Dear Editors,

We submit for your consideration "[Full manuscript title]," an original research
article for consideration in [Journal Name].

[2–3 sentences: what the study did, what it found, and the primary
implication — written for a reader who has not seen the abstract.]

This work addresses [specific gap or question] that is central to [the
journal's scope / a recent theme in the journal]. We believe it will be of
interest to [the journal's readership].

This manuscript has not been published previously and is not under
consideration elsewhere. All authors have approved the submitted version.
[Add any required declarations: ethics approval number, trial registration,
data availability statement, conflicts of interest.]

We suggest the following reviewers, who have relevant expertise and no
conflicts with our group: [Name, affiliation, email — three to five names].
We request that [Name] be excluded because [brief, factual reason].

We are available to provide any additional information and look forward to
hearing from you.

Sincerely,
[Corresponding author name]
[Title, institution]
[Email] | [Phone]
[ORCID: 0000-0000-0000-0000]

Keep the whole letter to one page. Editors receive many; brevity signals confidence.

Pre-submission readiness checklist

Desk rejections happen fast. Editors typically scan a submission for the most common failure modes before they even consider sending it to reviewers. Work through this checklist before you upload.

Scope and targeting

• [ ] The journal’s aims and scope explicitly cover this study type and topic
• [ ] The journal has published comparable work in the past two years
• [ ] Word count and article type match what the journal accepts

Manuscript preparation

• [ ] Title is specific and informative (not vague; no acronyms unexplained)
• [ ] Abstract is complete, within word limit, and structured as required
• [ ] Keywords match the journal’s preferred vocabulary or controlled list
• [ ] Reference style is correct throughout (format, punctuation, order)
• [ ] All figures and tables are cited in order in the main text
• [ ] Figure resolution meets the journal’s minimum requirement
• [ ] Statistical reporting is complete: effect sizes, confidence intervals, exact p-values (not “p < 0.05”)
• [ ] Reporting guideline checklist attached and referenced (see section below)

Declarations and compliance

• [ ] Ethics approval statement included (approval number + approving body)
• [ ] Informed consent statement included where applicable
• [ ] Clinical trial registration number stated in the abstract and title page
• [ ] All conflicts of interest declared by all authors
• [ ] Funding sources acknowledged with grant numbers
• [ ] Author contributions stated (CRediT roles)
• [ ] Data availability statement included

Submission package

• [ ] Title page is separate from the manuscript file (for blind review, where required)
• [ ] Author names and affiliations removed from the manuscript file itself (if double-blind)
• [ ] Cover letter addressed to the correct editor by name (check the journal website)
• [ ] Suggested reviewers with institutional emails ready (not Gmail or personal addresses)
• [ ] PDF proof generated by the submission system reviewed in full

If you are uncertain how your manuscript reads to a fresh expert eye, manuscript editing support and an AI pre-submission review can surface problems before the editor does.

Reporting guidelines: what they are and when they apply

Reporting guidelines are minimum standards for describing what you did in a study, so that readers can assess validity and other researchers can reproduce the work. Most major journals now require a completed guideline checklist as part of the submission package.

The main guidelines by study type

PICO (Population, Intervention, Comparison, Outcome) is a framework for framing clinical research questions rather than a reporting standard per se, but many journals expect it to be evident in the methods section of clinical and systematic review papers.

The EQUATOR Network (equator-network.org) maintains a searchable library of over five hundred reporting guidelines. Search by study type to find the one that applies.

When completing a checklist, point to the specific page and paragraph in your manuscript for each item — “Yes” without a location tells the editor nothing. If an item is not applicable, say so and explain briefly why. Checklists submitted as honest companions to the manuscript, rather than as a box-ticking exercise, earn goodwill with reviewers who know how to read them.

Understanding article processing charges and open access

Open-access publishing has become the norm in many fields, and understanding the cost structure matters before you submit.

Subscription journals

In a traditional subscription model, readers (or their institutions) pay for access. Authors typically pay nothing to publish, though some journals charge for colour figures in print, page charges for papers exceeding a length limit, or rush processing.

Open-access journals (gold OA)

Gold open-access journals make all content freely available immediately upon publication, funded by article processing charges paid by authors or their institutions. APCs vary widely — from a few hundred dollars at society journals to several thousand at journals from major commercial publishers. Before submitting, check:

• Whether your funder mandates open access (many now do, including NIH, Wellcome Trust, and most European research councils)
• Whether your institution has a read-and-publish agreement with the publisher that covers APCs
• Whether fee waivers are available (most publishers offer them for corresponding authors from low- and middle-income countries)

Hybrid journals

A hybrid journal operates on a subscription model but offers authors the option to pay an APC to make their individual article open access. Costs are typically the same as gold OA journals, sometimes higher.

Plan S and transformative agreements

If your work is funded by a Plan S-aligned funder, you are required to publish immediately open access with a CC BY licence. Check the journal’s compliance on the cOAlition S Journal Checker Tool before submitting to a hybrid journal, as compliance requirements vary.

Preprint servers

Posting to a preprint server (arXiv, bioRxiv, medRxiv, SSRN, etc.) before or during peer review is standard in many disciplines and does not constitute prior publication for most journals. Check the journal’s policy explicitly — it is usually in the author guidelines under “prior publication.”

What happens after you hit submit

Understanding the post-submission process removes much of the anxiety that comes with waiting.

Editor screening (1–5 business days)

The editor-in-chief or an associate editor reads the submission to determine whether it meets the basic threshold for peer review. They check scope fit, completeness of the submission package, apparent methodological adequacy, and ethical compliance. Papers that fail this check receive a desk rejection, usually with a brief explanation. A desk rejection is not a verdict on the quality of the science — it is a targeting signal. Revise the cover letter, recheck scope fit, and consider whether a different journal is a better match.

Peer review (typically 4–12 weeks)

If the paper passes editorial screening, it is assigned to two or three external reviewers with relevant expertise. Reviewers are volunteers; they are often slow to respond, slow to submit reviews, and sometimes decline after agreeing. The variation in review time across journals and disciplines is enormous. Most journal portals let you check status; if the status has not changed to “under review” after two weeks, it is reasonable to contact the editorial office to confirm the paper is moving.

The decision

Decisions typically fall into four categories:

• Accept — rare at first submission; most accepted papers have been revised
• Minor revision — specific, bounded changes requested; re-review is usually by the editor alone
• Major revision — substantial work requested; the revised manuscript typically goes back to at least some of the original reviewers
• Reject with invitation to resubmit — the paper is not accepted in its current form but the editors see sufficient merit to consider a substantially revised version; treat this as a major revision
• Reject — the paper is declined; unless the rejection letter invites resubmission, consider a different journal

When revising, write a detailed response letter addressing every reviewer comment individually. For each point, state what you changed and where in the manuscript — or explain clearly why you disagree and provide evidence. Reviewers are doing unpaid work; engage with them respectfully and substantively. Our guide to peer review covers how the review process works and what strong response letters include.

Frequently asked questions

How long should I wait before following up with the editorial office?

Allow at least six weeks from submission before contacting the editorial office to ask about status. Some fields have longer norms — check the journal’s stated review timeline in the author guidelines. When you do write, be brief and cordial: state the manuscript title and submission ID, note the submission date, and ask whether there is an expected timeline. Editors are generally willing to give a status update.

Can I submit to more than one journal at the same time?

No. Simultaneous submission — submitting the same manuscript to two or more journals concurrently without disclosure — violates standard publication ethics and the terms of almost every journal. It wastes reviewers’ time and can result in retraction if discovered after publication. Withdraw from one journal before submitting to another.

My paper was desk-rejected. Should I appeal?

Appeals are occasionally appropriate — for example, if the editor clearly misread the study design or scope. They are rarely successful and can slow your path to publication if the journal is unlikely to change its decision. A more productive use of time is usually to revise based on any feedback given and submit to a better-matched journal. Save your energy for the revision.

What should I put in the suggested reviewers field?

Suggest researchers who have published on the topic in the past three to five years, have no obvious conflicts (not your collaborators, former supervisors, or colleagues at your institution), and are at independent institutions. Include their institutional email addresses. Editors are not obliged to use your suggestions, but a thoughtful list of three to five names is useful to them and demonstrates professional maturity.

What is the difference between “reject” and “reject with invitation to resubmit”?

A standard rejection typically means the editors do not wish to see the paper again at this journal. “Reject with invitation to resubmit” (sometimes called “revise and resubmit” outside the formal decision hierarchy) means the editors see potential but want substantial changes before re-evaluating — it functions like a major revision but resets the submission formally. Read the decision letter carefully; the distinction is not always labelled clearly.

How do I know if a journal is predatory?

Legitimate journals are indexed in established databases (PubMed/MEDLINE, Scopus, Web of Science, DOAJ), have verifiable editorial boards with real researchers at real institutions, list transparent APCs, and do not solicit submissions by unsolicited email. If a journal approaches you out of nowhere with an unusually fast publication promise and unclear fees, verify it before submitting. Beall’s List (maintained informally by researchers) and Think Check Submit are useful reference points.

Submitting a manuscript is a skill that improves with practice, but each submission still carries risk: wasted weeks, a demoralising rejection, or — worse — publication in a venue that undersells the work. Doing the preparation well is the best investment you can make before you hit submit.

For researchers who want a rigorous read of their manuscript before it reaches a journal editor, PerfectPaper provides substantive AI-assisted feedback — argument structure, methods reporting, clarity, and consistency — in the same spirit a knowledgeable peer reviewer would. Start a free review before your next submission.

Related reading

• How to select the right journal for your paper — scope matching, impact, and avoiding predatory publishers
• Peer review explained — how the review process works and what reviewers actually look for
• Manuscript editing for academic papers — language, structure, and clarity before submission
• AI peer review tools — substantive pre-submission feedback
• Manuscript editing services — professional editing for journal-ready manuscripts
• Journal submission support — everything you need to submit with confidence