Methods and systems are described for detecting valve actuation faults in internal combustion engines operating in a skip fire operational mode. In one aspect, for each skip fire working cycle, an expected exhaust pressure is determined for a time period corresponding to a potential exhaust event. One or more exhaust gas pressure sensors are then used to measure an actual exhaust pressure during the potential exhaust period. The actual exhaust pressure is compared to the expected exhaust pressure to determine whether a valve actuation fault has occurred. A variety of valve actuation faults can be identified using the described approach. In some embodiments pressure sensors are deployed in the runners of the exhaust manifold.