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I don't see any native functionality to export highlighted notes made from within iBooks

Is there a third-party tool that will allow this?

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yes there is, if you have a mac.

Get iExplorer here

plug in your iOS device and use iExplorer to look in the books file and drag the following files to your desktop. iBooks.plist and iBooksData2.plist

and this app

put the files in the appropriate spot and you can get your highlights

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sweet, i will check this out. thanks for the suggestion – kenwarner Feb 3 '12 at 19:12

Sorry, but (at least currently) there's no way to do this.

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3rd party app Digested - does exactly what you need: "Quickly import bookmarks and notes from iBooks on iPhone, iPod, iPad, export to PDF and Evernote..."

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