A circuit design that contains at least two clock domains is simulated using a novel system and method for injecting the effects of metastability. The system includes detectors for detecting, during simulation, when a clock in a transmit clock domain and a clock in a receive clock domain are aligned and when the input of a register receiving a clock-domain-crossing signal is changing. The system includes coverage monitors for measuring, during simulation, statistics related to metastability injection. The system accurately models the effects of metastability by, at appropriate times during simulation, pseudo-randomly inverting outputs of registers receiving clock-domain-crossing signals. By accurately modeling the effects of metastability, errors in the circuit design can be detected while simulating a pre-existing simulation test. The simulation with metastability effects injection is repeatable and requires no modification of pre-existing RTL design files or simulation test files.