According to an article in Computerworld, Apple will charge $199 to replace the 95 watt-hour battery in the MacBook Pro with Retina Display, an increase of $70 from the traditional $129 that Apple charges for replacement batteries in the standard MacBook Pro and MacBook Air.
Before the introduction of the unibody MacBook Pro, all of Apple's notebooks had easily removable batteries. It made batteries quick to replace, but increased the complexity of the external case and the overall size of the machines. When the unibody machines were released, Apple designed a new type of battery that gave longer battery life and an increased number of charge cycles before the battery needed to be replaced:
Apple claims the Retina MacBook Pro's battery can be recharged 1,000 times before its charge capacity drops to 80% of normal.
Apple's standard 1-year warranty and the three-year warranty included with the AppleCare Protection Plan do cover batteries that have failed or have diminished capacity because "of a manufacturing defect". Apple's warranties do not cover a battery that has diminished capacity simply because it was charged many times.