This paper addresses the problem of comparing different variants of the same process. We aim to detect relevant differences between processes based on what was recorded in event logs. We use transition systems to model behavior and to highlight differences. Transition systems are annotated with measurements, used to compare the behavior in the different variants. Decision points in the transition system are also analyzed, and the business rules of the process variants in such points are compared. The results are visualized as colored transitions systems, where the colored states and transitions indicate the existence and magnitude of differences. The approach has been implemented in ProM, and the implementation is publicly available. The approach has been evaluated using real-life data sets. The results show how our technique is able to detect relevant differences that could not be captured using existing approaches. Moreover, the user is not overloaded with diagnostics on differences that are less significant.