Systems and methods are disclosed for comparing annotations in files to show changes in the annotations at a granular level. In one implementation, a system receives a first file and a second file for comparison. The system determines the annotation ranges for each annotation in the first file and the annotation range for each annotation in the second file. The system then determines the annotations from the first file that overlap with annotations from the second file and compares annotations that overlap. The system then incorporates the comparison of the annotations into a main comparison file. In certain implementations, the system uses an index to determine what annotations overlap. In other implementations, matched pairs are created from overlapping annotations.