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I have a Kindle 2 and I have some books I did not purchase from the Amazon store. Mostly PDFs, text files and .mobi files from other eBook stores.

Is there a way to export or otherwise back up my notes, highlights and bookmarks for those books?

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Connect the Kindle and copy the file documents/MyClippings.txt. That has all the highlighted text as well as the bookmarks and so on.

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You may use this small app to parse your 'My Clippings.txt' for Win and Mac.

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