When I click on the Word Count on the Review tab, the word count EXCLUDES the words contained in the header and footer. This word count also doesn't include the words contained in graphics or Drawing Canvases (unless they are in a Text Box AND you have ticked that option in the Word Count dialog).

Perhaps you could post a sample document that demonstrates what is not getting counted and we can work out whether it is due to the way you have structured your content.

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Andrew Lockton
Chrysalis Design, Melbourne Australia