A manuscript can be scientifically sound and still arrive at submission with inconsistent citations, missing details, or the wrong reference-list format. Fixing those problems by hand is slow—and the corrections can disappear the next time your citation manager reformats the document.
EndNote can handle most of this work, but only if you choose the right output style and check what it produces. Use the journal’s current author instructions as the source of truth. Use EndNote to implement those instructions.
This guide covers the EndNote 2025 desktop workflow for Microsoft Word on Windows. If you use macOS, EndNote Online, or Word Online, menu names and installation paths may differ; follow the corresponding versioned EndNote documentation.
What an EndNote output style controls
An EndNote output style is a set of formatting rules for citations and bibliographies. It can control author names, punctuation, title capitalization, journal names, year, volume, issue, page range, DOI placement, citation numbering, and reference-list order.
EndNote 2025 includes more than 7,500 bibliographic styles, although a typical installation includes only the most commonly used style files. The EndNote 2025 output-style documentation explains how styles work and links to the current Style Manager and installation instructions.
A style is not proof that your manuscript meets the journal’s requirements. Journals can revise their instructions, and a downloaded style can lag behind the current guidance. Treat the output style as an automation tool, then verify the result.
Format your references in six steps
1. Confirm the journal’s current instructions
Open the target journal’s author instructions before you change anything. Record the required citation system and inspect at least one reference example for each source type you use: journal article, book or chapter, website, dataset, software, or conference material.
Check details that software can format differently:
- numbered versus author–date citations;
- citation order versus alphabetical reference order;
- full versus abbreviated journal names;
- number of authors shown before “et al.”;
- title capitalization;
- inclusion of issue numbers, page ranges, article numbers, and DOIs; and
- treatment of online-first articles and web sources.
This outlet-first step is part of Sengi’s Share the Results workflow. If you are still choosing a target, start with Formatting Manuscripts for Ophthalmology Journals rather than configuring EndNote around a journal you may not submit to.
2. Select an installed style in Word
Open the manuscript in Word and find the EndNote tab. Use the Styles menu to select the journal’s style. EndNote states that this selection determines how it formats the document’s citations and bibliography and that you can change the style at any point.
If the journal is not visible in the short list, do not assume the style is missing. The list usually shows favorites, not every installed style.
After selection, inspect several citations and references. Confirm that EndNote reformatted both the in-text citations and the reference list. The current EndNote instructions for adding styles to the menu describe this workflow.
3. Find the style in Style Manager
In EndNote, go to Tools → Output Styles → Open Style Manager. Search for the journal or browse by category. You can preview an installed style and mark it as a favorite; favorite styles then appear in EndNote style menus, including Cite While You Write.
The EndNote 2025 Style Manager documentation gives the current Windows path and explains the search, preview, and favorite controls.
Match the journal name carefully. Similar titles, regional editions, and publisher families can use different formats.
4. Install a missing official style
If the style is not installed, use Get More on the Web from Style Manager or open EndNote’s official Style Finder. Search for the journal, download the style, and place it in the EndNote program Styles folder or your personal Styles folder.
The current Windows guide identifies the typical program folder as Program Files (x86)\EndNote 2025\Styles. A personal Styles folder may be easier to maintain if you do not have installation privileges. Restart EndNote after adding the file so the style list updates. Follow the full EndNote 2025 installation instructions rather than relying on an older screenshot.
Then return to Style Manager, mark the style as a favorite, and select it in Word.
5. Modify only what the journal requires
If no exact style exists, compare a close style with the journal’s current examples. EndNote permits you to modify an existing style or create a new one. Before editing, identify the exact mismatch: author display, bibliography template, punctuation, sorting, journal abbreviation, or another defined rule.
Do not rebuild a style because one reference is wrong. First check the underlying EndNote record. Missing pages, an incorrect reference type, a title pasted in all capitals, or an absent DOI cannot be fixed reliably by changing the output style.
When a genuine style change is necessary, preserve the original and label your custom copy clearly. Test the custom style on several reference types, not one convenient example. If your team shares the manuscript, share the approved style file and record which version you used.
If EndNote is not the right tool for the team’s systems or collaboration model, compare the workflow with Choosing the Right Citation Manager Software or the current Mendeley Cite style guide. Do not mix instructions from one product into the other.
6. Run a final reference check
Automation reduces repetitive formatting; it does not remove the need for review. Before submission, sample the reference list against the journal’s instructions. Include different source types and inspect:
- author sequence and initials;
- article and source titles;
- journal abbreviation;
- year, volume, issue, pages, or article number;
- DOI or URL treatment;
- citation sequence and bibliography order; and
- one-to-one correspondence between in-text citations and reference-list entries.
Correct bad source data in the EndNote library, then update the document. Reserve style edits for true formatting-rule differences.
For an investigator-initiated trial manuscript, also confirm that the cited protocol, registry record, primary outcome sources, statistical methods, and safety references are the intended versions. That is an editorial control, not a feature EndNote can decide for you.
Keep the workflow maintainable
The weakest reference workflow depends on screenshots and memory. A stronger workflow records four things: the target journal, the date its instructions were checked, the EndNote style name or custom file, and the person who completed the final comparison.
That small record matters when a manuscript changes journals or returns months later for revision. You can see what was configured, what must change, and what should not be rebuilt.
Take the next step
Reference formatting is one part of a larger publication decision. Eye-Dea to Impact places it within Share the Results: select the outlet early, align the manuscript with its requirements, and preserve a clear path from trial question to reported result.
