A diagnostic control system for an internal combustion engine including a discrete variable valve lift (DVVL) system includes a first module that determines a knock threshold value based on engine operating parameters and an engine knock sensor that generates a knock signal. A second module monitors a portion of the knock signal that is associated with a particular cylinder of the engine, selectively identifies a fault of at least one valve of the DVVL system associated with the particular cylinder based on the portion and the knock threshold, and outputs a fault signal corresponding to the particular cylinder.