Yes, TOCs only pick up headings etc in the body of the document. The STYLEREF field can be used to pick up the content of a given Style in the body of the document and replicate it in the header or footer.

As for using hyperlinks in the TOC, TOCs are hyperlinked by default, even though they don't look like hyperlinks, and there should be no need to try to add them manually. In any event, even if you do add them manually, they'll be deleted next time the TOC is updated.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]