How do I add a table of contents to an EPUB in Calibre?

Open the EPUB in Calibre's book editor (right-click → Edit book). Go to Tools → Table of Contents → Edit Table of Contents → click 'Generate TOC from major headings'. Calibre rebuilds both the NCX (EPUB 2) and NAV (EPUB 3) documents from H1/H2/H3 heading tags in your chapter files. Review the entries, click OK, and save. The TOC will appear in all EPUB readers.

Why does my EPUB have no table of contents?

The most common cause: no heading tags (H1/H2/H3) in the chapter HTML files. EPUB TOCs are generated from heading elements. PDFs converted without layout analysis often lack headings — all text becomes plain paragraphs, so no TOC is generated. Fix by adding heading tags in Sigil or Calibre's editor, then regenerating the TOC. toolkit.bot detects headings automatically during PDF conversion.

Does KDP require a table of contents in EPUB?

KDP strongly recommends a working TOC and will flag EPUBs with missing or empty navigation as quality issues. EPUBs without a TOC may publish but often receive a lower quality score. Kobo Writing Life and Apple Books Connect reject EPUBs that fail EPUBCheck validation, which includes TOC requirements. Draft2Digital auto-generates a TOC if none is present.

What is the difference between NCX and NAV in an EPUB?

NCX (toc.ncx) is the EPUB 2 navigation format — a separate XML file listing chapters and page numbers. NAV (nav.xhtml) is the EPUB 3 navigation format — an HTML file with the required epub:type='toc' section. EPUB 3 requires NAV; NCX is optional but included for compatibility with older readers. Calibre and Sigil generate both when you rebuild the TOC.

Guides › The EPUB format · Published 11 Jun 2026 · Updated 2 Sep 2026 · toolkit.bot

How to Add or Fix a Table of Contents in an EPUB (Calibre and Sigil)

A working table of contents is essential for EPUB distribution — KDP, Kobo Writing Life, and Apple Books all require a navigable TOC. If your EPUB has a missing or broken TOC, here's how to fix it in under 10 minutes.

How EPUB Tables of Contents Work

EPUB 3 uses two TOC components:

NCX file (toc.ncx): The EPUB 2 navigation document — still required by some older readers and some publishing validators
NAV document (nav.xhtml): The EPUB 3 navigation document — required for EPUB 3 compliance and used by modern readers

Both are generated automatically from heading tags (H1, H2, H3) in your chapter HTML files. No heading tags → no TOC entries. This is why PDFs converted without heading detection produce EPUBs with empty TOCs. Each entry points to a chapter file, optionally with an anchor (chapter2.xhtml#section1), and entries can nest so sub-sections appear indented under their chapter.

The TOC is also an accessibility requirement: EPUB Accessibility 1.1 requires a navigation document with a TOC, because screen-reader users rely on it to jump between chapters instead of paging linearly. A missing or broken TOC is an accessibility failure, not just a store rejection.

Method 1: Rebuild TOC in Calibre

Open Calibre. Add your .epub file.
Right-click → Edit book (opens Calibre's built-in editor).
In the editor, go to Tools → Table of Contents → Edit Table of Contents.
Calibre shows the current TOC. Click Generate TOC from major headings to rebuild from H1/H2/H3 tags automatically.
Review the generated entries — add, remove, or reorder as needed.
Click OK, then File → Save.

This regenerates both the NCX and the NAV document. If your chapter files don't have heading tags, the TOC will still be empty — you'll need to add headings first (see below).

Method 2: Build TOC in Sigil

Open Sigil (free, sigil-ebook.com). Open your .epub.
Go to Tools → Table of Contents → Generate Table of Contents.
The TOC editor shows detected headings. Choose which heading levels to include (H1, H2, H3), drag to reorder, check/uncheck to include or exclude entries.
Click OK. Sigil writes the NCX and NAV files.
Save the EPUB (Ctrl+S).

Adding Heading Tags to Chapter Files

If your EPUB has no headings (common in PDFs converted without layout analysis), you'll need to add them before generating a TOC:

In Calibre's editor or Sigil, open each chapter HTML file in Code View.
Find the chapter title text (currently a <p> tag) and change it to <h1> (main chapters) or <h2> (sub-sections).
After adding headings to all chapters, regenerate the TOC using the steps above.

Common TOC Problems After PDF Conversion

Every chapter at the same level. The converter found headings but ignored nesting. In Calibre's TOC editor, drag entries onto a parent to indent them; in Sigil, edit nav.xhtml and wrap sub-entries in a nested <ol>.
Entries read "Chapter 1 ........ 12". The PDF bookmarks carried dotted leaders and page numbers. In Sigil open toc.ncx, use Edit → Find & Replace in Regex mode with the pattern *\.{2,}.*$ and an empty replacement.
Entries jump to the wrong place. Page-based anchors from the PDF do not survive reflow. Regenerate the TOC from headings instead of trying to preserve the original links.

TOC Requirements for KDP, Kobo, and Apple Books

Amazon KDP: Requires a working NCX or NAV. KDP's EPUB validator will flag a missing or empty TOC as a warning. An EPUB with no TOC may still publish but will get a lower quality score.
Kobo Writing Life: Requires a functional NAV document (EPUB 3). EPUBs without a TOC are rejected or require manual review.
Apple Books Connect: Requires a valid NAV document. EPUBs are checked with EPUBCheck — a missing TOC fails validation.
Draft2Digital: Generates its own TOC from chapter structure, but having a pre-built TOC improves accuracy.

Preventing the Problem at Conversion

If you're converting a PDF to EPUB, use a converter that detects heading structure — this is what generates automatic TOC entries. toolkit.bot uses layout analysis to identify font size, bold, and position patterns to detect headings. The resulting EPUB includes a working TOC without any manual work.

Convert at toolkit.bot/pdf2epub — the EPUB output includes both NCX and NAV documents with entries for all detected chapter headings.

Need an EPUB with a working table of contents from your PDF? toolkit.bot detects headings automatically.

Convert PDF to EPUB →