We’ve gone over a number of ways to assist in accessible navigation by improving the structure and semantics of your content, but navigating at the content level is only a complement to a good table of contents. EPUB 3 includes a new declarative means of creating tables of contents called the navigation document, which is a fancy way of saying that you can now create a special kind of XHTML document for reading systems to provide their own built-in navigation mechanism(s).
Note that the navigation document is not necessarily the same as the table of contents at the start of the book or at the beginning of a section. The navigation document is primarily intended for reading system use, but can also be included as content if it can serve both roles.
Declarative tables of contents are not new to EPUB 3, however. EPUB 2 had a file format called the NCX for this purpose, which was taken from the DAISY talking book standard (and that format can still be included in EPUB 3 publications for forwards compatibility with older reading systems). But the NCX was a complex solution to a much simpler problem, and actually hindered accessibility in this new context, as its lack of intrinsic display controls led to navigation levels being chopped off to improve visual rendering.
So, to strike back up on a common theme, not all markup is created equal, and the quality of your table of contents for navigation is a reflection whether you put the full structure of ...