You can use the Articles panel in CS6 and above (not sure in CS5.5 or below?) to setup your reading order.
If you have any other queries on this please let me know
thankyou for your response but the articles panel is exactly what i am having issues with. I have a 30 page document broken into sections with headings and subheadings etc. Presently each page has its own article, is this correct? The export process ignores the article panel order completely.
@Daniel – how do you export to PDF then?
And maybe most important: What exact version of InDesign on what OS are you using?
If you are looking around on the web, you can see that there is a 3rd party plugin that can assist you on creating tagged PDFs with InDesign.
Here a review in InDesignMagazine:
And here a guide using this:
Especially see: "Task 7: Create tagged PDF file" and read it carefully.
There are some hints on possible bugs with tagged PDFs exported from InDesign.
For inspecting tagged PDFs in Acrobat Pro there is a free tool over here: