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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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up vote 3 down vote accepted

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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This one parse automatically the code, you can add custom tags on it. It is free unless you need to retrieve your clippings from the iphone kindle app (in this case you would need a paid chrome app).

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See the blog article

In short you just need to upload your myclippings.txt to Step by Step instructions on the blog article

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