Systems and methods for identifying and managing the relationships between clock domains in an integrated circuit design are disclosed. A computer-implemented method analyzes the behavioral structure of the clock-to-clock logical relationships in a proposed integrated circuit design. In one embodiment, the method comprises receiving as inputs a description of the design (in a synthesizable format or a synthesized gate-level netlist and definitions of the clock waveforms and timing constraints used in the design, and automatically identifying the relationships between the clocks specified in the description and categorizing the relationships into a plurality of behavioral categories. A list of timing exceptions may optionally also be provided as an input. The identified relationships between clocks and the behavioral categories may be used to verify any existing timing exceptions between clock pairs, and/or to create any missing exceptions between the clock pairs.