Some things to try:
1. Make sure you've installed the iBooks app on your iPad. It doesn't come automatically installed. It's a free download in the iTunes App Store.
2. You may need to change your sync settings. Open iTunes with your iPad connected to your computer. Select your iPad from the list of devices on the left side of the screen. Then click the "books" tab near the top of the screen. Make sure that "sync books" is selected. Then apply that setting and sync your iPad.
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