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I have a video with chapter markers in iMovie HD 6.03 (267.2).

What settings do I need to use when exporting to get a file with chapter markers viewable by QuickTime and iTunes?.

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Have you tried doing this? I am fairly certain that the chapter markers would go into any of the quicktime/itunes filetypes. – Jamie Aug 18 '11 at 14:35
I am pretty sure that @Jamie is right. – daviesgeek Aug 18 '11 at 18:25
Unfortunately, I am pretty sure @Jamie is wrong because I just tried it. Note that the OP is using iMovie 6, a very old version of iMovie. I've never managed to make it export chapters to anything but iDVD. – Kyle Jones Mar 6 '14 at 19:05

Looks like you can do it using Metadata Hootenanny.

It allows you to edit and search the metadata that can be stored in QuickTime movies (mov files), including chapters. Quicktime files support a large number of metadata options, but the QuickTime Player doesn't provide an easy way of accessing them. Metadata Hootenanny does.

You can read this forum thread for more info.

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