How to Use EndNote: A Researcher’s First-Project Walkthrough

This page is about EndNote, the reference-management software from Clarivate — the desktop application you use to store references, attach PDFs and generate a bibliography. It is not about the endnote feature built into Microsoft Word (the note that appears at the end of a document, inserted from Word’s References tab > Insert Endnote, keyboard shortcut Alt+Ctrl+D on Windows). Those are two unrelated things that share a name. If you came looking for Word’s note feature, you want Microsoft’s own footnotes and endnotes documentation, not this page. It is also not about EndNote Click, the free browser extension Clarivate rebranded from Kopernio, which retrieves full-text PDFs and is a separate product with its own account.

Version and platform, stated up front. The steps below describe EndNote 2025 (Clarivate’s current desktop release) on Windows and macOS, checked against Clarivate’s own EndNote 2025 documentation and university library guides in August 2026. EndNote 21 behaves the same way for almost everything here, and libraries created in EndNote 2025 open in EndNote 21 and vice versa. Where a step genuinely differs between Windows and macOS, it is called out inline rather than described as if one interface were universal — that difference is real and is where most stuck researchers get stuck.

What this walkthrough produces

Most EndNote instruction is a feature tour. This is a single first project, run end to end, finishing at a manuscript you can actually attach to a submission form: a library that will survive, references imported cleanly from a database, PDFs attached and grouped, in-text citations live in Word, the bibliography reformatted for a specific journal, and a plain-text copy with the field codes stripped. Six steps.

Two of those steps are effectively irreversible, and they are the two that decide whether the project survives: where you put the library file (step 1) and when you convert to plain text (step 6). Everything else can be undone. If you read nothing else, read those two.

If you have not chosen a tool yet, do that first — this page assumes EndNote is already decided, usually because your institution holds the licence. For the choice itself see Zotero vs. EndNote and the wider reference-management software comparison.

Step 1 — Create the library (and put it somewhere that will not corrupt it)

In EndNote, File > New, name the library, choose a location. What you get is not one file: you get an .enl file and a folder of the same name ending in .Data, which holds the attached PDFs, figures and the search index. This is still true in EndNote 21 and EndNote 2025. The two must stay together in the same folder. Moving, renaming or emailing the .enl on its own gives you a library with every reference intact and every attachment gone — the single most common self-inflicted EndNote failure.

Do not store the library in a folder that syncs to the cloud — Dropbox, OneDrive, Google Drive, iCloud Drive — or on a network/shared drive. Clarivate’s support material and every university guide checked say the same thing, because the failure mode is specific: a file-sync client writing to the .enl while EndNote also has it open can corrupt the database, and the corruption is often not visible until much later. If you need the library on two machines, use EndNote Sync to an EndNote Web account, which is designed for exactly this; do not let a sync client do it behind EndNote’s back.

Keep one library, not several. The instinct to make a library per project is wrong here — EndNote’s grouping features (step 3) are what separate projects, and multiple libraries mean duplicate records, split PDFs and a Cite While You Write session pointing at the wrong one. To move a library between machines by hand, use File > Compress Library (.enlx), which packages the .enl and .Data into a single transportable file.

Step 2 — Get references in from a database

There are four routes in and they are not equally good.

1. Direct export from the database (do this one). Run your search in Web of Science, Scopus, PubMed, Embase or your discipline’s index, select results, and use that database’s own export-to-EndNote option. The metadata arrives with the field mapping the database intends, which is the highest-fidelity route available.
2. RIS or other tagged files. Where a database offers no direct EndNote export, download an .ris (or BibTeX, or a tagged text file) and use File > Import > File, choosing the matching import filter. Choosing the wrong filter is the usual cause of authors landing in the title field — if the imported records look scrambled, the filter is the first thing to check, not the database.
3. Online Search from inside EndNote. The left-hand pane lets you query selected databases directly. Convenient for grabbing one known item; weaker than direct export for a real search, because EndNote’s connection files expose a reduced version of the database’s search interface. Do not run a systematic search this way — see Boolean search operators for literature searching.
4. From a PDF. Importing a PDF that carries an embedded DOI will usually create a reference from it. Scanned PDFs and older articles without embedded metadata will not work, and the fallback is fetching structured metadata from the DOI or typing it in.
5. Manual entry. References > New Reference opens a blank record where you pick a reference type and type every field yourself. Slowest route and the one most exposed to typos, but it is the only option for material with no exportable record at all — an archival document, a personal communication, an older print source cited from the physical item. Use it as a last resort, not a starting habit.

Before you go further, deduplicate. Two databases will overlap. Library > Find Duplicates compares records and lets you keep one. Doing this at import time costs minutes; doing it after you have cited forty references costs an afternoon.

Step 3 — Attach PDFs and organise

Find Full Text (right-click selected references) attempts to retrieve PDFs using your institution’s subscriptions. It works through your library’s link resolver, so it retrieves what you are entitled to and silently fails on what you are not — an empty result is usually a licensing answer, not a bug. EndNote 2025 supports up to 45 file attachments per record, so a reference can carry the article, the supplementary material and your own notes together.

Organising uses three overlapping mechanisms, and knowing which is which prevents a mess:

• Groups — manual collections. A reference can sit in several groups at once; adding it to a group does not copy or move the underlying record.
• Smart groups — saved searches that populate themselves as matching references arrive. Good for a standing topic within a long project.
• Tags — added in recent versions, colour-coded, applied per reference and independent of group membership. Useful as a workflow state (read / to read / cited) rather than as a subject classification.

For a first project, one group per manuscript plus tags for reading state is enough. If several people will work in the same library, stop and read citation management software for a research group first — shared libraries have licensing and ownership consequences that are much easier to get right at the start.

Step 4 — Insert citations in Word with Cite While You Write

Cite While You Write (CWYW) is the Word add-in that inserts live, field-coded citations and rebuilds the bibliography as you go. It installs with EndNote Desktop and appears as an EndNote 2025 tab in Word’s ribbon. If that tab is not there at all — or vanishes after an Office upgrade — the repair is a different dialog on each platform; see installing Cite While You Write in Word for the Windows and macOS paths in the order to try them.

Compatibility, precisely. CWYW requires Word 2016, 2019, 2021 or Microsoft 365, on Windows or macOS. On macOS it works with the locally installed desktop Word only, and is also compatible with Apple Pages. Word Online and Google Docs are supported through EndNote Web, and only for EndNote 2025 and EndNote 21 users — if you are on an older desktop version, browser-based writing is not an option and no amount of reinstalling will make it one.

The working loop is short: put the cursor where the citation goes, use Insert Citation, search, insert. To change a citation after the fact — adding a page number, suppressing the author, removing it — use Edit & Manage Citation(s). Do not edit the grey citation text or the bibliography by hand. Those are Word fields owned by EndNote; typed edits are silently overwritten the next time the document reformats, and hand-editing the bibliography is the reason a reference list stops matching the in-text citations.

Platform difference worth knowing: macOS adds a separate EndNote menu in Word containing Settings and the Customizer, which is where a Mac user reinstalls a missing CWYW toolbar. Windows has no Customizer — the equivalent repair is the COM add-in route in the troubleshooting table below.

EndNote 2025 also adds Find a Journal and a Paperpal integration to CWYW, and a Research Assistant AI feature in EndNote and EndNote Web. Treat AI-suggested references the way you would any other unverified source: open the record and confirm it exists before citing it. See citation management with AI writing tools for where these tools actually fail.

Step 5 — Switch the output style for your target journal

The output style is the rule set that turns your stored records into formatted citations and a formatted reference list. Changing it reformats the entire document — this is the payoff for having done steps 1 to 4 properly, and it is why the bibliography must never be hand-edited.

From the style dropdown on the EndNote tab in Word, pick the style; if the journal is not in the short list, choose Select Another Style… to search the full installed set. EndNote ships with a large library of styles and more are downloadable from Clarivate’s style download page — the exact count varies by version and is not worth memorising. Install a downloaded .ens file by opening it in EndNote and using File > Save As into your Styles folder.

Do not trust the style name. A style called after a journal encodes that journal’s requirements as of whenever the style was last maintained, and journals change their instructions more often than styles get updated. Before submission, check the formatted output against the journal’s current author instructions — author-count cut-off before et al., whether article titles are sentence case, whether DOIs are included and in what form. The style is a starting point, not an authority. Background on the underlying conventions: citation styles and referencing formats, Vancouver referencing style, and et al. citation rules. If the target venue is not settled yet, how to choose a journal comes before this step, not after.

Step 6 — Produce the submission copy (Convert to Plain Text)

Publishers routinely require manuscripts with reference-manager field codes removed, because live fields interfere with their production and conversion systems. EndNote’s own tool for this is Convert to Plain Text.

Windows and macOS, same path: on the EndNote 2025 tab in Word, select Tools, then Convert to Plain Text. Click OK in the confirmation dialog. EndNote creates a new document containing the same text with the codes stripped; save that copy under a new filename.

What you lose, stated plainly: Clarivate’s documentation says of the copy, “The copy does not contain Cite While You Write field codes, so you cannot reformat with Cite While You Write.” The converted document has no connection to your EndNote library. Adding a reference, reordering the list or switching style later cannot be done in that file — you go back to the original, redo the change, and convert again.

So the sequencing rule is absolute: convert last. Finish the writing, finish the reference list, set the final style, then convert — and keep the original field-coded document, permanently, as the master. Every revision round after peer review is done in the master, not the plain-text copy. A useful naming discipline is to keep the master under an unambiguous name and give each converted copy the submission date, so nobody on a co-authored paper edits the wrong file.

macOS has a second, blunter option some guides mention: select all with ⌘+A and press ⌘+6 to strip all Microsoft Word field codes (the number-row 6, not the keypad). This removes every Word field, not only EndNote’s, and Clarivate warns it “irretrievably remove[s] the links between your document and your EndNote libraries.” Use Convert to Plain Text instead unless you have a specific reason not to, and back up first either way.

What breaks, and the fix

Symptom	Likely cause	Fix
No EndNote tab in Word (Windows)	The COM add-in is disabled	Word: File > Options > Add-ins, set Manage to COM Add-ins, click Go, tick EndNote Cite While You Write, OK, restart Word.
No EndNote tab in Word (macOS)	CWYW not installed into this Word profile	Use the EndNote menu > Customizer to reinstall Cite While You Write, then quit and reopen Word.
Library opens but all PDFs are missing	The .Data folder was left behind when the .enl was moved or emailed	Restore the .Data folder alongside the .enl. To transfer in future use File > Compress Library (.enlx).
Library behaves erratically or reports corruption	Stored in a cloud-synced or network folder	Move it to a local drive and use EndNote Sync for multi-machine access. Recover from your most recent .enlx backup if damaged.
Reference list does not match in-text citations	The bibliography was edited by hand	Undo the manual edits; correct the underlying record in EndNote, then reformat. Never type into the bibliography field.
Imported records have authors in the title field	Wrong import filter for that file	Delete the imported set, re-import with the filter matching the source database’s export format.
Co-author cannot reformat your document	They lack the references locally	The field-coded document carries a traveling library — the co-author can export those references into their own EndNote library from the EndNote tab before reformatting.
Cannot use CWYW in Word Online or Google Docs	Older desktop version	Browser-based CWYW runs through EndNote Web and is available to EndNote 2025 and EndNote 21 users only — this is a version limit, not a fault.
EndNote misbehaving after a macOS upgrade	Version predates the OS	EndNote 20 and earlier were not designed for macOS Tahoe; Clarivate’s advice is to upgrade to EndNote 2025.

Where EndNote sits in the rest of your workflow

A reference library is one input to several downstream tasks it does not itself perform. Your EndNote library is not a publication record — for that, see adding publications to your ORCID record and compiling one complete publication list across indexes. Author-name disambiguation when importing from Web of Science is its own problem: Web of Science author search. Reading notes belong somewhere with more structure than a reference record — see note-taking methods for research — and the synthesis itself is a separate skill covered in how to write a literature review. This page is part of CASRAI’s research tools cluster.

If you decide EndNote is not the right tool after all, the equivalent walkthrough for the main open-source alternative is Zotero for researchers, with Zotero setup and troubleshooting for the install-and-repair layer. If your institution licenses a web-based manager instead, see RefWorks. Migrating out of EndNote is well-trodden: export as EndNote XML or RIS, import on the other side, and check a sample of records — EndNote XML preserves more metadata than RIS if you use custom fields or long notes.

Frequently asked questions

Is EndNote free?

No. EndNote is commercial software from Clarivate. Many universities hold a site licence that gives staff and students the desktop application at no personal cost, so check your library’s software page before buying — that licence is the usual reason a researcher is using EndNote rather than a free alternative. A limited EndNote Web account is available separately from the full desktop product.

What is the difference between EndNote and EndNote Web?

EndNote (or EndNote Desktop) is the installed application on Windows or macOS. EndNote Web — also called EndNote Online — is the browser-based companion your desktop library syncs to. Sync is also what makes the library available on a second machine, and what enables CWYW in Word Online and Google Docs for EndNote 2025 and EndNote 21 users.

Can I use EndNote on Linux?

There is no native Linux desktop client; EndNote Desktop is Windows and macOS only. EndNote Web works in a browser on any operating system, but without the desktop application you lose the local library and the Word add-in.

Do I have to remove field codes before submitting?

Check the journal’s author instructions — many publishers ask for it explicitly, and it is safe practice regardless because live fields can behave unpredictably in a publisher’s conversion pipeline. Do it last, and keep the field-coded original.

Can I open an EndNote 21 library in EndNote 2025?

Yes. Libraries created in EndNote 21 open in EndNote 2025 and libraries created in EndNote 2025 open in EndNote 21, so a lab running mixed versions is not blocked. Feature availability still differs by version — Word Online and Google Docs support, for instance, requires EndNote 21 or 2025.

Should I keep one EndNote library or one per project?

One. Use groups, smart groups and tags to separate projects inside it. Multiple libraries produce duplicate records, split PDF attachments, and Cite While You Write sessions pointing at the wrong library — all of which are more work than the organisation they were meant to save.

Where should I store my EndNote library?

On a local drive, never in a Dropbox / OneDrive / Google Drive / iCloud folder or on a network share. Use EndNote Sync for access from a second machine, and File > Compress Library (.enlx) for backups and hand transfers.

Sources checked

Steps and version claims on this page were checked in August 2026 against Clarivate’s EndNote 2025 documentation (including the Windows and macOS pages on removing field codes) and against university library guides that maintain EndNote instruction — among them UCL. Clarivate’s own product pages are the authority on anything that has changed since; where a menu label has moved in a point release, the linked documentation wins over this page. Licence pricing is deliberately not quoted here because it varies by institution, seller and region.