How to Properly Use Footnotes and Endnotes in Markdown

Academic essays, legal documents, and detailed reports often require parenthetical commentary. Adding footnotes and endnotes lets authors include supplementary explanations, secondary sources, or source attributions without disrupting the readability of the primary text.

In this guide, we will cover how to format, organize, and compile footnotes and endnotes in markdown workflows.

Footnotes vs. Endnotes: What’s the Difference?

While both options display supplementary content, their placement differs:

• Footnotes: Appear at the bottom of the exact page where the corresponding citation occurs.
• Endnotes: Compiled as a single list at the very end of the document, section, or chapter.

Markdown engines handle the positioning of these components automatically during the export process.

Footnote Syntax in Standard Markdown

Most modern Markdown compilers (including Pandoc, GitHub Flavored Markdown, and common Javascript parsers) support the square-bracket caret syntax ([^key]) to represent notes.

To create a footnote, add a marker in your paragraph text:

This research builds upon the foundational studies conducted in 2018[^1]. 
Another claim requires a descriptive anchor tag[^note-details].

Then, define the footnotes anywhere in the document (usually at the very bottom of the file):

[^1]: See Smith et al., "Understanding Computational Limits," Journal of Science (2018).
[^note-details]: The dataset used for this calculation is available under the MIT license.

The compiler will replace the markers with sequential, clickable numbers (e.g. [1], [2]) in the body text and link them to their definitions at the page bottom.

Inline Footnotes

If you prefer to write the note content right alongside the text without separating the definition, Pandoc allows inline footnotes:

Here is some main text ^[This is an inline footnote that will compile to the page bottom.].

Multi-Line Footnotes

If your footnote needs multiple paragraphs, lists, or code blocks, indent subsequent lines by four spaces:

[^multiline]: This is the first paragraph of the note.

    - Bullet points inside footnotes are allowed.
    - Keep them indented by four spaces.
    
    This is the second paragraph.

Converting Footnotes to Endnotes with Pandoc

If you compile your Markdown using Pandoc and want the footnotes to display as endnotes at the end of the document instead of the bottom of each page, you can customize your LaTeX settings.

In your YAML header, use the footglist or endnotes package configuration:

---
header-includes:
  - \usepackage{endnotes}
  - \let\footnote=\endnote
---

And place \theendnotes at the end of your Markdown file where the list should compile.

Styling Footnotes with CSS Paged Media

For web-based HTML-to-PDF compilation engines, footnotes can be styled to stick to the bottom of the page container. Weasyprint, for instance, supports page footnotes through the float: footnote CSS standard:

span.footnote {
  float: footnote;
}

@page {
  @footnote {
    border-top: 1px solid #e2e8f0;
    margin-top: 10px;
    padding-top: 5px;
  }
}

This transforms elements matching <span class="footnote"> directly into page-anchored footnotes.

Refine Your Research Layouts

Footnotes and endnotes keep your text readable while maintaining academic transparency. If you are looking for an online environment that lets you write, test Markdown notes, and export professional PDFs in one click, try our Markdown to PDF Editor.