Methods and systems are described for detecting valve actuation faults in internal combustion engines operating in a skip fire operational mode. In one aspect, a torque model is used to estimate an expected net torque during a selected operating window. The torque model considers an expected torque contribution from each of the cylinders and accounts for the effects of specific skip fire firing decisions that affect the expected torque contribution from each cylinder. A parameter indicative of the actual engine torque is also measured. Valve actuation faults can then be identified based at least in part on a comparison of the measured parameter to an expected parameter value that is based at least in part on the expected net torque. With the described approaches, the occurrence of the valve actuation fault can be made within one engine cycle of the initial occurrence of the fault.