Every writer working in plain text hits this the same way. You have a claim that needs a source, or an aside too good to cut and too tangential to keep, so you reach for a footnote — and discover that Markdown, the actual specification, has no such thing.
What it has instead is a collection of extensions that mostly agree with each other, implemented by roughly half the tools you will pass the file through.
Why footnotes are the awkward case
A footnote is not a piece of text. It is a piece of text plus a promise about where it will appear: at the bottom of the page carrying the reference. That promise is only meaningful in a medium that has pages.
| Medium | Has pages? | What a footnote can mean |
|---|---|---|
| Printed book | Yes, fixed | Bottom of this page — the classic form |
| Yes, fixed | Bottom of this page, if the renderer supports it | |
| EPUB | No — text reflows | A popup, or a link to the back. Never "the bottom of the page" |
| Web page | No | A link down the document |
This is the same distinction that decides almost everything about the two formats. An EPUB has no page bottoms to put anything at: the reader sets the type size, and the text falls where it falls. Every e-reader therefore turns footnotes into something else — usually a tappable popup, sometimes a jump to a notes section — and it makes that decision for you.
What the `[^1]` syntax actually does
The syntax people reach for comes from PHP Markdown Extra and was adopted by Pandoc, GitHub and several static site generators. It looks like this:
The first print run was withdrawn within a week.[^1]
[^1]: Hale, *A Short History of Errata*, p. 214.Where it is supported, that renders a superscript marker and collects the note. Where it is not — and that includes plenty of converters, editors and preview panes — it renders as literal text, brackets and caret included, in the middle of your paragraph. Nothing warns you. You find out when you open the export.
- Pandoc supports it, and will place real footnotes when producing a paginated format through LaTeX.
- GitHub supports it and links to the bottom of the file.
- CommonMark, the specification most tools claim to follow, does not include it at all.
- bukpress renders the syntax it documents and passes anything else through as text — which is the honest failure mode, but it is still text you did not want on the page.
The method that works in both formats
Number your notes by hand, keep them in a back-matter section, and reference them in the text with a plain marker. It sounds primitive next to an extension that renumbers automatically. It is also the only approach that produces the same book from every tool you will ever use.
The first print run was withdrawn within a week (1).
---
## Notes
### Chapter One
1. Hale, *A Short History of Errata*, p. 214.
2. The withdrawal notice is reproduced in full in Appendix B.- Number within chapters, not across the book. Note 47 in chapter nine is a number nobody can hold; note 3 of chapter nine is findable. Restart at 1 in each chapter and head each group with the chapter name.
- Pick one marker form and keep it.
(1)and[1]are both fine. Mixing them across a manuscript is the kind of inconsistency a reader notices without being able to say why. - Put the notes section before the index and after the appendices, which is where conventional back matter puts it and therefore where a reader looks.
- Renumber only at the end. Doing it while the chapter is still moving is wasted work, twice.
When a note should not be a note at all
Most footnotes in a first draft are one of three things, and only one of them deserves the apparatus.
| What it is | Where it belongs |
|---|---|
| A source for a factual claim | A numbered endnote — this is the real case |
| An aside you enjoyed writing | In the paragraph, or cut |
| A definition of a term | A glossary, or the sentence that first uses it |
| A link to something online | Named in the text, with the URL in the notes |
| A caveat the argument depends on | The body text. If it matters, say it |
The middle row is the one worth being strict about. An aside in a footnote is a small negotiation with the reader: leave the sentence, read this, come back. In a printed book that costs an eye movement. In an EPUB it costs a tap, a popup, a dismissal, and finding your place again. If it is good enough to keep, it is usually good enough to fold into the paragraph.
Citations, if you have a lot of them
A book with fifty sources is a different problem from a book with five. At that volume, keep a plain reference list in one file, in a consistent style, and cite in the text by author and year — (Hale, 2019) — with the full entry in a Bibliography section at the back. No numbering to maintain, no renumbering when a chapter moves, and the reader can look something up without counting.
- Pick a style and be consistent rather than correct. Unless a publisher has specified one, internal consistency is what a reader perceives as rigour.
- Alphabetise the bibliography by surname. It is the only order anyone can search by eye.
- Include access dates for anything online, because the other half of those links will be dead within three years.
- Keep the list in the manuscript, not in a separate reference manager the export cannot see.
Whichever route you take, the reason to settle it early is the same reason to settle heading structure early: notes are the sort of thing that seems trivial for eight chapters and then takes a full day to normalise across a finished manuscript. One decision, made once, in plain text that every tool understands.