Footnotes vs. Endnotes: How (and Where) to Use Them in Your Book

One of the most common questions I hear from nonfiction authors (and some fiction authors, too) is whether they should use footnotes or endnotes—and what the difference actually is. And while it might seem like a small formatting choice, your decision can have a significant impact on how your book is perceived. If you’re aiming to publish professionally, especially in print, there are good reasons to consider this carefully.

What follows is more than just a technical overview. I want to provide some context for how readers experience footnotes and endnotes, how typesetters handle them, and what to expect if you plan to publish your book across multiple formats. We’ll also touch on some real-world pitfalls I’ve seen while working with authors at Foglio, and how we help correct them before they make it to print.

Let’s start with the basics, then move on to the deeper issues—like how this decision affects your reader, your credibility, and your workflow.

What’s the Difference Between Footnotes and Endnotes?

At their most basic, footnotes appear at the bottom of the page on which the reference is made. Endnotes, by contrast, are compiled at the end of a chapter or at the end of the book. Both systems serve the same general purpose: to give the reader more information without cluttering the main body of the text.

That additional information might include citations for quoted material, explanatory asides, background context, translations, or even your own commentary. The format you choose should reflect the reading experience you want to create.

Why the Choice Matters

Footnotes have the advantage of immediacy. They keep everything within reach, and for certain types of nonfiction—academic writing, historical essays, detailed memoirs—this can be a benefit. You don’t have to flip back and forth to chase a citation. This is especially helpful for readers engaging with dense material.

That said, footnotes can also be distracting. Visually, they add clutter to the page. Too many of them can undermine the rhythm of your prose, and they don’t always translate well to smaller print sizes or screen readers.

Endnotes clean up the page. They’re more elegant in many types of books, particularly those that are narrative-driven. If you’re writing a memoir, creative nonfiction, or even a heavily researched book that still prioritizes readability, endnotes offer a way to offload necessary information without slowing your reader down.

Where It Gets Complicated: Print vs. Digital

If you’re publishing in print only, footnotes are relatively straightforward. A good typesetter will format them to match the rest of the page layout, keeping them unobtrusive but accessible. But the minute you add an ebook version, things shift.

In EPUBs and other digital formats, footnotes can behave unpredictably depending on the device or reading app. Some reading platforms convert them to clickable popups, others send the reader to the end of the chapter. This experience is often clunky, particularly for older readers or anyone not familiar with navigating digital notes. That’s why for ebooks, endnotes (linked to chapter sections or a back-of-book reference) are almost always the better choice.

The Role of Citation Styles

The style you choose—Chicago, MLA, APA, or a custom house style—may dictate the format of your notes. For trade books and popular nonfiction, you can usually opt for the structure that best fits your content. But if you’re writing academic work, check your institution’s or publisher’s guidelines. Some are strict about where and how citations appear.

Either way, clarity is key. Inaccurate or inconsistent notes can undermine your credibility. I’ve worked on more than a few manuscripts where the note numbers didn’t match the references, or where the formatting changed halfway through the book. These issues are frustrating for readers and a red flag to reviewers.

What About Dual Systems?

Some books use both. Footnotes for brief clarifications, endnotes for formal citations or longer digressions. While this can work, it has to be handled with care. The danger is that you create a system that’s internally inconsistent, which leads to confusion.

If you’re working with Foglio on your typesetting or formatting, this is something we’ll help guide you through. In some cases, we’ve even created dual-edition workflows: one optimized for print with footnotes, another for digital with a carefully linked endnote structure.

Typesetting Considerations

From a technical standpoint, footnotes in InDesign are easier to manage than many people think—but only if everything is properly styled from the beginning. Manually added notes (where the author types everything at the bottom of the page) don’t adjust dynamically. So when your manuscript reflows, those footnotes end up in the wrong place or even on the wrong page.

At Foglio, we use professional tools to ensure footnotes are tied to the text and remain consistent across different layout scenarios. This is also one reason why clean manuscript preparation matters. If you’re submitting your manuscript with placeholder citations, make sure you clearly label them and keep a separate notes file. This will help streamline the typesetting process and prevent delays.

Endnotes, while easier to wrangle during typesetting, come with their own design challenges. They require space—either at the back of the chapter or in a dedicated section. If your notes are long, this can add significant page count. It’s also important to cross-reference them properly, using clickable links for digital formats and clearly marked superscripts or numerals in print.

Common Pitfalls (and How to Avoid Them)

One of the most common issues I see is formatting inconsistency. Authors sometimes use multiple types of notation in the same manuscript: asterisks, superscripts, parentheticals. This usually happens when content has been copied and pasted from different sources, or when early drafts weren’t fully edited. The result is a jarring reading experience and a nightmare to clean up in typesetting.

Another issue is overuse. Some authors use notes to clarify every minor point, which can overwhelm the reader. Notes should support the text, not compensate for it. If you find yourself constantly clarifying something in a footnote, it might be worth revisiting how that point is explained in the main body of the manuscript.

You also need to be mindful of legal issues if you’re quoting from outside sources. As we’ve noted in our blog post on proofreading practices, quoting more than a few lines can trigger the need for formal permissions. Your notes section is not a loophole.

Footnotes and Endnotes in eBooks

This is an area where formatting gets tricky. In a print book, the footnote sits quietly at the bottom of the page. In an ebook, the equivalent might be a hyperlink, a pop-up, or an entirely different screen. Not all platforms handle these the same way, and it’s not always clear to the reader what to expect.

That’s why when we convert your manuscript to EPUB, we make sure your notes function seamlessly. Endnotes tend to be more consistent across devices, and we always test across the major platforms before final delivery.

The video below demonstrates the use of pop-ups for parallel translations, which could also be used for footnotes and endnotes. It’s a fairly robust method of adding interactivity to an ebook that works with nearly every e-reading device.

Here’s an example if interactive pop-ups in an ebook, in this case used for parallel translation. The same could be done for footnotes, endnotes, and citations.

Final Thoughts

Whether you choose footnotes or endnotes depends on your content, your audience, and your publishing goals. In either case, consistency, clarity, and formatting integrity matter more than anything else. You’re not just conveying extra information—you’re shaping the way your readers engage with your material.

We’ve helped hundreds of authors through this process, from first drafts to finished books, and it’s always worth slowing down at this stage to get the notes right. If you’re unsure about what direction to take, or if your notes are already a mess and you need help cleaning them up, we’re here.

Book a free consultation if you want help figuring out the best structure for your footnotes, endnotes, or anything else in your book.

And if you’re still working on your manuscript, check out our beta reader questionnaire to help gather thoughtful feedback before moving on to formatting.

Your notes are part of your voice. Let’s make sure they reflect that.