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Books only sync via iTunes until 9.3. In iTunes you need to select which you want to sync to each device
 
As the above poster mentioned. I looks will allow iCloud sync when iOS 9.3 releases. But just to clarify even further. Your Mac will also require 10.11.4 for the updated iBooks. Once both are on 10.11.4 and 9.3, any PDF or book added into iBooks on your computer will show up and sync to your iPad and iPhone via iCloud.
 
This is great news! Any idea when 10.11.4 and 9.3 are going to be released?

Also do you have a source for this information?

> Don't worry, I did a search for both. Soon is the answer!
 
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