After you install OS X Mavericks and open iBooks for Mac for the first time, iBooks for Mac automatically moves your book library from iTunes over to the iBooks for Mac app. When you browse your Book library in iTunes 11.1 or later, iTunes notifies you that your books have been moved to iBooks for Mac. After clicking OK, you no longer see Books as a category in the media list in iTunes. Future book purchases made from the iBooks Store through iTunes or iBooks are downloaded to your iBooks library instead of iTunes.
Note: This applies only to a Mac with OS X Mavericks installed. If you have a Windows PC or a Mac that is using OS X Mountain Lion or earlier, you continue to browse and purchase books through iTunes. To read books you will need to sync your books to an iOS device with iBooks for iOS installed by either downloading past book purchases, enabling auto-download of books onto your iOS device, or tethering your iOS device to your computer.
Note: If you have multiple iTunes libraries on your Mac, you'll need to load each library into iTunes, and then launch iBooks to move the books from that library to iBooks. You'll need to repeat this for each iTunes library file. Learn more about opening alternate iTunes libraries.