Here is proof that the iPhone 5S will have a fingerprint scanner. The image on the left is the reported internals of the 5S and the image on the right is the internals of the iPhone 5. If you look at the highlighted areas you will see two different types of connections. The one of the right has been the standard home button style since the iPhones inception. The one left is a flex cable connection that is typically used for more complex data transfer i.e. information from a fingerprint scanner.