This study investigates how and why experienced programmers annotate program code. Research has shown that marking up prose with a pen is an invaluable aid to reading for understanding. However program code is very different from prose: there are no studies on how programmers annotate code while reading. We asked experienced programmers to read code printed on paper and observed their annotation practices. We found the main reasons for annotating code are to assist with navigation and to record information for later use. Furthermore, we found annotation practices that are hard to replicate in current standard Integrated Development Environments. This suggests that support for digital ink annotations in programming tools may be useful for comprehending program code.