Format your notes once, with the built-in footnote tool in whatever you write in, and let the ebook file carry links that run both ways: from the marker to the note, and from the note back to the marker. Do that and print gets footnotes at the foot of the page, while every ebook platform gives the reader a working note, whether as a pop-up or as a linked endnote.
What Do Readers Actually See on Each Platform?
Print is straightforward: footnotes sit at the foot of the page and endnotes collect at the end of the chapter or the back of the book, exactly as you would expect. Ebooks are where the variation starts, because reflowable text has no fixed page and therefore no bottom of the page to put a footnote on. What the reader gets instead depends on the reading app.
The mechanism that makes a note behave well is a pair of labels written into the ebook file. (EPUB is the standard ebook format every non-Kindle store uses, and the one Amazon converts from.) The EPUB 3 Structural Semantics Vocabulary, republished by the W3C in May 2026, defines footnote as “ancillary information, such as a citation or commentary, that provides additional context to a referenced passage of text,” used on the <aside> element, which is the HTML container for content set apart from the main flow, and noteref as “a reference to a note, typically appearing as a superscripted number or symbol in the main body of text,” used on a link. Written into an EPUB, they look like <aside epub:type="footnote"> for the note and <a epub:type="noteref"> for the marker in the text.
Reading systems that recognise those markers can show the note as a pop-up panel. Ones that do not treat the note as ordinary page content and display it as a linked endnote instead. That is a progressive enhancement, not a fork in the road: the pop-up is the upgraded experience and the linked endnote is the baseline that works everywhere, and both come out of the same file.
Why your file now needs two labels, not one
One requirement has changed since this article was first written: a note now wants two labels rather than one, doing two different jobs. The first, epub:type, tells the reading app to make a pop-up. The second, an ARIA role, tells a screen reader what the element is. EPUB 3.3, which became a W3C Recommendation in January 2026, carries an explicit caution about epub:type: those values “do not enhance access through assistive technologies like screen readers as they do not map to the accessibility APIs. Only ARIA roles influence how assistive technologies understand such elements.” The EPUB Accessibility Techniques note states the consequence directly: leaving out the ARIA roles reduces accessibility for assistive technology users, while leaving out the epub:type values costs you reading-system features such as pop-up footnotes.
The roles themselves come from DPUB-ARIA 1.1, the W3C’s set of role names for the parts of a digital publication: role="doc-footnote" goes on the note and role="doc-noteref" goes on the marker in the text. Every formatting tool covered below writes the epub:type values. Whether it also writes the ARIA roles varies, which is worth asking your formatter about if accessibility matters to your book.
A related change: the singular term endnote was deprecated in June 2025, in both the Structural Semantics Vocabulary and DPUB-ARIA, so a note should be labelled footnote wherever it physically sits. The plural endnotes, for the section that collects them, remains current.
Platform by platform
Here is what each major platform publishes for an EPUB containing correct markup and links running both ways, and where we could not trace a published answer.
| Platform | What the reader gets | Source |
|---|---|---|
| Kindle (KDP) | Pop-up panel on devices such as Kindle Paperwhite. Links must run both ways whether or not <aside> is used, and Amazon recommends putting the note text at the end of the chapter or book | KDP Text Guidelines – Reflowable |
| Apple Books | Pop-up overlay. Requires the epub:type pair, plus the EPUB namespace (a one-line declaration at the top of each file) on the <html> element | Apple Books Asset Guide 5.3.1 |
| Kobo (e-ink and iOS) | Pop-up box containing the note, including images and links on iOS | Kobo’s published EPUB spec |
| Kobo (desktop, Android, Windows) | Linked note, no pop-up; the reader follows the link | Kobo’s published EPUB spec |
| Nook (B&N Press) | Linked note, according to Vellum’s documentation, which states pop-ups are not available on Nook. B&N’s own guide says only “ideally, footnotes should be linked” and we could not trace a B&N statement about pop-ups | B&N Press ePub Formatting Guide; Vellum help |
| Google Play Books | Pop-up, according to Vellum’s documentation, which lists Google Play among the platforms showing them. Google’s own published EPUB 3 feature table does not list notes, and we could not trace a Google statement on them elsewhere | Vellum help |
The two Kobo rows are worth a second look, because the split falls the opposite way round from what the hardware suggests. Kobo’s own EPUB specification says pop-ups appear on the e-ink readers and on iOS, and that “on the Desktop, Android and Windows platforms users will not see a pop-up but can simply follow the link.” It is the apps on the larger screens that fall back to a plain link, not the small e-ink devices.
Kobo’s spec also documents a trap worth knowing about. A hyperlink that carries no epub:type at all will still open as a pop-up on Kobo’s iOS and e-ink platforms if it points at a target inside the same EPUB, that target holds at least nine characters of text, the target is under 5,000 characters, and it appears later in the book than the link. That is how an ordinary cross-reference ends up behaving like a footnote.
The practical takeaway has not changed: one EPUB with the right labels and links running both ways serves every platform.
How Should You Handle Footnotes in Microsoft Word?
If your manuscript is in Microsoft Word, its built-in note system is the thing that makes everything downstream possible. Use References > Insert Footnote or Insert Endnote and Word numbers them automatically: footnotes at the foot of each page, endnotes at the end of the section or document depending on the setting in the Footnote and Endnote dialog. Either can be converted to the other at any point.
What Word cannot do is produce an EPUB. It writes .docx and PDF, so Word is almost always stage one of a two-stage process: you author in Word, then either upload the .docx to a retailer that converts it, or run the file through a formatting tool that builds the EPUB.
If you are publishing on KDP only
Uploading the .docx to KDP is the shortest route, and KDP still accepts Word files and converts them: its supported-formats page lists DOC and DOCX, with the caveat that “some files with complex formatting may not convert as well.” The conversion will attempt to turn Word footnotes into notes with links running both ways, and the results vary from manuscript to manuscript, with return links and duplicate markers the usual casualties. Preview the converted file in Kindle Previewer and open several notes, checking each time that you can get back to where you were.
This route produces a Kindle ebook and nothing else. It gives you no EPUB for Apple Books, Kobo or anywhere else.
If you are publishing wide
Publishing beyond Kindle needs an EPUB, and Word cannot make one alone. The common routes are these.
Word to Vellum. Import the .docx and Vellum reads Word’s footnote markers and converts them automatically. This is the path with the least manual work.
Word to Atticus. Import the .docx, but the notes have to be in Word’s default footnote style rather than endnotes. If your manuscript uses endnotes, convert them first in Word.
Word to Calibre or Sigil. Convert the .docx to EPUB in Calibre, then tidy the result in Sigil. This gives full control but requires you to be comfortable reading and editing the file’s underlying code, so it is the specialist route rather than the default one.
Converting notes inside Word
Microsoft’s own documentation gives the path for turning footnotes into endnotes and back: open the References tab, click the small dialog launcher arrow at the corner of the Footnotes group, then click Convert. The Convert Notes menu offers three choices, not two: convert all footnotes to endnotes, convert all endnotes to footnotes, or swap them. The References tab and dialog launcher work the same way on Mac.
Word for the web is the exception. Microsoft’s current guidance says you can insert notes in the browser but “if you want to convert footnotes to endnotes or the other way around, use the Open in Word command and convert them there.” Plan to do the conversion in the desktop application.
Print and ebook from one Word file
Keep footnotes in your Word master for print. When it is time to build the ebook, copy the file first and work on the copy, never the master, then either import the copy into a formatting tool or convert the notes there. If a professional formatter is producing the files, hand over the master with its footnotes intact and say that you want the ebook to carry notes with links running both ways. For more on managing the two formats together, see producing both a paperback and ebook from one Word manuscript.
What Does Vellum Do With Footnotes?
Vellum handles the print-to-ebook note problem with the least author intervention of any tool here: you insert a footnote in the editor and Vellum decides the rest per format. It runs on Mac only, requires macOS 13 or newer, and is sold as Vellum Press at $249.99 for ebooks and paperbacks or Vellum Ebooks at $199.99 for ebooks alone.
What Vellum produces
Print. Footnotes appear at the foot of the page and endnotes at the back of the book. You choose per note, or convert them all at once from the gear menu in the note editor.
Ebook. Vellum writes EPUB 3 with the aside epub:type="footnote" markup and links running both ways. Its own documentation states that “on ebook platforms like Kindle, Apple Books, and Google Play, footnotes are presented as popups,” and that “popups aren’t available on Nook and on some Kobo devices,” where “clicking a footnote indicator will take the reader to a list of footnotes at the end of a chapter.” Both layers go into every EPUB it generates, with nothing to configure.
If you are publishing on KDP only
In Vellum, generate the Kindle file from File > Generate Books and upload it to KDP directly. Pop-up notes work across Kindle devices and apps. That file is Kindle-only, so you will need a separate EPUB from the same project if you later go wide.
If you are publishing wide
Vellum can generate platform-specific files, or a single Generic EPUB for an aggregator such as Draft2Digital. Vellum’s documentation is explicit that for the Generic file, “popup support requires that you leave EPUB 3 output enabled” in Generation Settings, so check that before exporting. One file then covers every platform.
Print and ebook from one Vellum project
Producing both formats from one project is Vellum’s default behaviour. The same project produces a print PDF with footnotes at the foot of the page and an ebook with pop-ups or linked endnotes according to the reader’s device, with no conversion step and no second file to maintain.
Choosing the note indicator
Vellum offers four indicator styles: symbols (*, †, ‡), which is the default for new books, numbers, roman numerals and letters. Symbols suit a book with a few notes per chapter; numbers are easier to follow in heavily annotated non-fiction. Vellum warns that changing the footnote indicator may change the endnote indicator too, to stop the two clashing. Its documentation also draws a useful line on which to use: footnotes for “ancillary information, like an explanation or a comment,” endnotes for citations.
How Does Atticus Handle Footnotes and Endnotes?
Atticus asks you to decide note placement explicitly for each format, where Vellum decides for you. It costs $147 as a one-time purchase and runs on Windows, Mac, Linux and Chromebook.
What Atticus produces
Print. Three options in the Formatting tab: footnotes at the foot of the page, notes at the end of the chapter, or notes at the end of the book.
Ebook. The foot-of-page option is not offered, and Atticus says why: “Since eBooks don’t have traditional pages, you cannot set footnotes in the ePub version of your book; it is restricted to the print version.” You choose end-of-chapter or end-of-book instead, and Atticus generates links running both ways in either case, so the reader can reach the note and return. Whether Kindle or Apple Books then renders those as pop-ups depends on the markup in the export, so check the preview on your target platform rather than assuming.
If you are publishing on KDP only
Export the EPUB from Atticus and upload it to KDP. Choose end-of-chapter or end-of-book placement based on how the book reads: end-of-chapter suits books with many notes, end-of-book is cleaner where citations are occasional.
If you are publishing wide
The same EPUB serves every platform.
Print and ebook from one Atticus project
Set placement to Footnotes for print and to End of Chapter or End of Book for the ebook, both in the Formatting tab. Atticus applies the split when you export each format from the one project.
Importing from Word
Atticus imports Word footnotes, with conditions it states plainly. The notes must be in Word’s default footnote style, so convert endnotes to footnotes in Word before importing. Every note must be “under 1000 characters,” and empty notes cause export problems, so check for both in Word’s Show Notes pane before importing a heavily annotated manuscript. Atticus also advises creating each new note with the toolbar button rather than copying and pasting an existing one, because every note carries an identifier the EPUB’s internal navigation depends on, and a duplicated identifier breaks the link.
What Are the Footnote Options in Adobe InDesign?
InDesign gives the most typographic control over notes of any tool here and takes the most skill to use, which is why it is normally the typesetter’s tool rather than the author’s. It runs on Windows and Mac and is sold only as part of an Adobe Creative Cloud subscription, so there is no one-time price to compare with the other two. It is also the only one of the four where print footnote positioning, ruling, spacing and numbering restarts are all adjustable.
What InDesign produces
Print. Full footnote support with detailed control over placement and appearance, plus native endnotes, which InDesign has had since the CC 2018 release.
Ebook. The reflowable EPUB export dialog offers three footnote placement options, named exactly: “End of the section (Endnotes),” “After paragraph,” and “Inside a Pop-up (EPUB3).” The pop-up option writes the EPUB 3 aside markup with links running both ways, so capable readers show an overlay and others fall back to a linked note at the end of the section. Two things to watch: the export dialog’s EPUB version menu offers only 2.0.1 and 3.0, and the pop-up option requires the 3.0 setting.
If you are publishing on KDP only
In InDesign, export to EPUB 3.0 with the pop-up footnote option selected, then upload that file to KDP.
If you are publishing wide
Use the same EPUB 3.0 export with the pop-up footnote option selected. The file passes through an aggregator to retailers unmodified.
Print and ebook from one InDesign file
Keep footnotes in the document for the print PDF, and choose the pop-up option at EPUB export. For a heavily annotated academic book, InDesign’s native footnote-to-endnote conversion handles the change in the document itself, with cross-reference links intact. Older guides point to a third-party conversion script for this job; that script is still online but is now labelled as being for versions before CC 2018 and kept for historical purposes, so the native feature is the current route.
Which Footnote Mistakes Break an Ebook?
Five faults account for the broken notes that turn up most often, and each one has a check you can run before you upload.
Missing return links. The marker in the text links to the note, but the note does not link back. KDP’s Text Guidelines are unambiguous: “Regardless of whether the aside element is used, Amazon requires formatting footnotes with bidirectional hyperlinks.” Without the return link, a Kindle pop-up may not appear at all, and on a platform that shows a linked note the reader is left in the notes section with no way back. KDP’s Guide to Kindle Content Quality lists “an unlinked footnote” among the issues readers report. Every tool in this guide writes both links automatically; the fault appears when EPUB files are assembled by hand, or when a .docx is uploaded to KDP without anyone checking the preview.
Making ordinary links bidirectional. This is the mirror image of the last one and it is easy to do by accident. KDP’s Hyperlink Guidelines warn that “to avoid unintended footnote pop-ups, internal links that are not footnotes should not be formatted with bi-directional hyperlinks,” and recommend that a non-footnote link go from A to B and on to C rather than back to A. A cross-reference built the wrong way starts opening as a pop-up, which is the same behaviour Kobo’s spec documents from its side.
Manual footnotes instead of the built-in tool. Some authors type a number and the note text at the foot of a Word page by hand rather than using Insert Footnote. Those notes carry no structural information, so no formatting tool and no retailer can turn them into working ebook notes, and they do not renumber when a note is added or removed. Use the built-in feature in whatever you write in.
Mixing footnotes and endnotes in one manuscript. Pick one system. Mixed numbering confuses readers and produces unpredictable results in ebook conversion.
Empty note markers. Deleting a note’s text in Word without deleting its superscript marker leaves a blank note behind. Atticus names these as a cause of export failures, and they show up as empty pop-ups on Kindle, which KDP’s pre-publication checklist asks you to look for. You cannot search for an empty note, because there is no text to find. In Word, switch to View > Draft and open Show Notes to see every note in one pane, then scroll it: an empty one appears as a number with nothing after it.
Footnotes used as a literary device. If your novel uses them in the manner of Terry Pratchett or Susanna Clarke, test the ebook on more than one device before publishing. A pop-up works well for a short aside and becomes intrusive when the notes are frequent, and some novelists convert literary footnotes to inline parenthetical text for the ebook edition rather than accept that.
Endnotes are also part of your book’s back matter structure. Deciding where the notes section sits relative to the bibliography, the acknowledgements and the about-the-author page produces a better reading experience than adding it at the end as an afterthought. If your EPUB passes validation on one platform but produces errors on another, the note linking structure is among the first things worth checking.
The three habits underneath all of this
Use the built-in note tool rather than typing notes by hand. Keep the links running in both directions. Preview the result on a device rather than in the software that made it. Everything else on this page is detail hanging off those three.
Frequently Asked Questions
If I format footnotes for pop-ups, will readers on Nook or Kobo still see the notes?
Yes. Pop-up footnotes are a progressive enhancement rather than an either/or choice. Where the platform supports them the reader gets an overlay; where it does not, the same file shows the notes as linked notes at the end of the chapter. Kobo’s own specification puts pop-ups on its e-ink readers and iOS app, with desktop, Android and Windows following the link instead. The links running both ways are what make navigation work in every case, so one file serves all platforms.
Can I use footnotes in a Kindle ebook?
Yes. Amazon’s Text Guidelines for reflowable books say Amazon requires footnotes to be formatted with bidirectional hyperlinks whether or not the aside element is used, and that on devices such as Kindle Paperwhite those notes are displayed in a pop-up. Amazon also recommends placing the note text at the end of the chapter or book for a better reading experience. If the return link is missing, the pop-up may not appear and the reader is sent to the notes section instead.
Should I use footnotes or endnotes for a non-fiction ebook?
Notes collected at the end of the chapter or book, with links running both ways, are the safest universal choice, because they work everywhere without depending on pop-up support. If you write in Vellum you can keep footnotes in the manuscript and let it produce pop-ups on supported readers and linked notes elsewhere. The requirement that actually matters is that a reader can reach the note and get back, whatever device they are on.
How do I convert footnotes to endnotes in Microsoft Word?
Open the References tab, click the small dialog launcher arrow at the corner of the Footnotes group, then click Convert. The Convert Notes menu gives three options: convert all footnotes to endnotes, convert all endnotes to footnotes, or swap them. The path is the same on Windows and Mac. Word for the web cannot do the conversion; Microsoft’s guidance for the browser version says to use Open in Word and convert there.
Do I need different EPUB files for different platforms?
No. A single EPUB 3 file with links running both ways works on all of them, and the reading platform decides the presentation. If you use Vellum you can optionally generate platform-specific files, but its Generic EPUB also works for aggregator distribution through Draft2Digital or IngramSpark, provided EPUB 3 output is left enabled so the pop-up markup survives.
Do footnotes need ARIA roles as well as epub:type?
They serve different purposes and current W3C guidance is to use both. EPUB 3.3 notes that epub:type values do not map to accessibility APIs and that only ARIA roles influence how assistive technologies understand an element. The EPUB Accessibility Techniques note adds that omitting the roles reduces accessibility for assistive technology users, while omitting the types costs reading-system features such as pop-up footnotes. In practice that means role=”doc-footnote” on the note and role=”doc-noteref” on the marker, alongside the epub:type values. Ask your formatter whether the export writes both.
