Switching EndNote to a Numbered Style in Word (Vancouver, IEEE)

This page is about EndNote, the reference-management software from Clarivate — specifically the Cite While You Write (CWYW) add-in for Microsoft Word. It is not about Word’s own built-in endnote feature (References tab > Insert Endnote). If you got here looking for that, see Microsoft’s footnotes and endnotes documentation instead. This guide covers one specific task: taking a document already written with EndNote CWYW in an author-date style and switching it to a numbered style — Vancouver, IEEE, or a journal-specific numbered variant — and what to do when the citations do not renumber the way you expect.

What actually changes when you switch to a numbered style

An author-date style (APA, Chicago author-date, Harvard) shows a name and year at each citation point and lists the bibliography alphabetically. A numbered style — Vancouver, IEEE, Nature, Cell, and most biomedical and engineering journal styles — replaces every in-text citation with a number, assigns that number by order of first appearance in the document, reuses the same number every time that same source is cited again, and lists the bibliography in that same number order rather than alphabetically. Switching styles is not a cosmetic reformat: EndNote has to walk the entire document, work out the first-appearance order of every unique reference, assign or reassign numbers accordingly, and rebuild the bibliography list in that new order. That is the step that goes wrong when a “style switch” looks like it did not take.

To change the style itself: on the EndNote tab in Word, use the style dropdown, or Select Another Style… if the numbered style you need is not in the short list — Vancouver and IEEE both ship with EndNote by default. For background on the numbering and formatting rules Vancouver specifically follows, see Vancouver referencing style; for how citation styles differ as a category, see citation styles and referencing formats. If your target journal needs a style that is not in EndNote’s bundled set, that is a separate installation task from what this page covers — the style dropdown only helps once the style file already exists on your machine.

The normal path: switching style with Instant Formatting on

By default, EndNote’s Instant Formatting is on once you have inserted your first citation. Clarivate’s own documentation states plainly what it does: “Instant Formatting works while you write your paper. As you insert citations, EndNote uses the currently selected style to format citations and update the bibliography.” That same continuous scan is what fires when you pick a new style from the dropdown — with Instant Formatting on, choosing Vancouver or IEEE should immediately renumber every in-text citation and rebuild the bibliography in the new number order, with no extra step. If that is what happens for you, you are done; the rest of this page is for when it is not.

Forcing a full renumber: Update Citations and Bibliography

Instant Formatting has a real cost on a long document — EndNote is rescanning the whole file on every edit — so it is common practice, and something Clarivate itself recommends, to turn it off for large manuscripts (dissertations, systematic reviews, anything running past a few dozen pages) to keep Word responsive. If Instant Formatting is off, changing the style dropdown updates the setting but does not automatically walk the document and renumber anything. That is the single most common reason a style switch to Vancouver or IEEE “does nothing.”

The fix is the same command either way: on the EndNote tab in Word, run Update Citations and Bibliography. This forces EndNote to rescan every field-coded citation in the document from the top, reassign numbers in first-appearance order under the now-selected style, and rebuild the bibliography to match. Run it any time you have changed the style, reordered content, added or deleted a citation, or simply are not sure the numbering is current — it is a safe, repeatable operation with no side effects on your stored library.

Why the renumbering broke — the actual causes, not just “try updating again”

If you have already run Update Citations and Bibliography and the numbering is still wrong, the cause is almost always one of these:

• Citations typed or pasted as plain text. CWYW can only see, format, and renumber citations that carry an EndNote field code — the ones you inserted through Insert Citation from an open library. A citation typed by hand, or pasted in from another Word document as plain text, has no field code, so it is invisible to the renumbering pass: it will not get a number, and it will silently throw off the first-appearance order for every citation after it. The fix is to delete the plain-text citation and re-insert it properly with Insert Citation.
• The wrong library — or no library — is open. Field codes point to specific records in a specific .enl library, not to text. If you open the document on a different machine, or with a different library open, without the matching library loaded, EndNote cannot resolve the citations and you will see “?” or “Impossible to Locate Reference” placeholders instead of numbers. Open the correct library first, then run Update Citations and Bibliography again.
• A record was edited or deleted in the library after it was cited. If the underlying reference was removed or its record ID changed, the field code that used to resolve to it no longer does. Use Edit & Manage Citations on the EndNote tab to see which specific citation is broken and relink or re-insert it from the current library.
• Track Changes is on during a full reformat. CWYW reformats against the document’s actual text, and tracked insertions/deletions can confuse what it treats as “current” content, especially across a full renumber on a long, heavily-edited manuscript. Accepting or finishing pending edits before running Update Citations and Bibliography avoids this.
• Co-authors are working from different libraries. If a document has been merged from sections drafted by different people against their own separate EndNote libraries, some field codes will point to records that simply do not exist in whichever single library is open when you renumber. Everyone needs to be citing from the same shared or synced library — see how to use EndNote for the library-first workflow this depends on.

Vancouver and IEEE numbering are not identical

Both are “numbered by first appearance, number reused on repeat citation” styles at the core, but the on-page formatting differs by style file, not by some universal numbered-style rule EndNote applies automatically:

• Vancouver citations appear as either a plain or superscript Arabic numeral, and which one a target journal wants is a house-style choice within the Vancouver family, not something the name “Vancouver” fixes on its own — see Vancouver referencing style for the numbering and reference-list rules in full.
• IEEE citations appear in square brackets, e.g. [1], again numbered by first mention and reused at every repeat.

If a switch to “a numbered style” produces the wrong bracket type, superscript when the journal wants inline parentheses, or vice versa, that is very often the wrong specific style file selected in Select Another Style… — Clarivate and many journals maintain more than one numbered variant, and picking the exact one your target venue names (rather than “Vancouver” or “IEEE” generically) matters. Adjusting a numbered style’s own numbering behavior at the template level — for example, whether a style resets numbering or keeps it consecutive — is a Style Manager task, not something this page covers in depth; treat that as a separate step from the day-to-day style switch and renumber this guide is about.

Before you submit: spot-check the renumbered document

After a style switch and an Update Citations and Bibliography pass, check three things before moving on: every in-text citation shows a number, with no “?” or “Impossible to Locate Reference” placeholders left anywhere in the document; the bibliography is ordered by first in-text appearance, not alphabetically; and a citation used more than once shows the same number every time. Only once the numbering is confirmed correct should you run Convert to Plain Text for submission — converting removes the field codes those checks depend on, so any further style change or renumber has to happen before that step, not after. The full submission-copy procedure, including exactly what Convert to Plain Text does and does not preserve, is covered in how to use EndNote.

Frequently asked questions

Does switching styles in EndNote always renumber citations automatically?

Only when Instant Formatting is on. With Instant Formatting off — common on long documents, since Clarivate recommends disabling it there for performance — changing the style dropdown updates the setting but does not walk the document, so nothing renumbers until you run Update Citations and Bibliography manually.

Why do some citations show a question mark after I switched to a numbered style?

Almost always a broken link between the citation’s field code and your EndNote library: the wrong library (or no library) is open, or the underlying record was edited or deleted after it was cited. Open the correct library and use Edit & Manage Citations to relink the specific broken entries.

How do I force EndNote to fully renumber a document?

Run Update Citations and Bibliography from the EndNote tab in Word. It rescans every field-coded citation, reassigns numbers in first-appearance order under whichever style is currently selected, and rebuilds the bibliography to match.

Is Vancouver numbering the same as IEEE numbering?

Both number citations by first appearance and reuse the number on repeat citation, but the on-page formatting differs: Vancouver typically renders as a plain or superscript numeral depending on journal house style, while IEEE renders in square brackets. Picking the exact style variant your target journal names, not just “Vancouver” or “IEEE” generically, is what determines which formatting you get.

What if a citation was pasted in as plain text instead of inserted from EndNote?

It will not participate in renumbering at all, because it carries no EndNote field code — CWYW can only see, format, and number citations inserted through Insert Citation. Delete the plain-text citation and re-insert it from the open library.

Reference-manager mechanics verified against Clarivate’s own EndNote 2025 documentation (docs.endnote.com) and cross-checked against the CASRAI EndNote install/usage guides below. Journal-specific numbering conventions (bracket style, superscript vs. inline) vary by venue — always confirm against the target journal’s current author instructions before submission.