An engine control system for a homogenous charge compression ignition (HCCI) engine includes an airflow determination module and a sensor diagnostic module. The airflow determination module generates a first plurality of estimates of airflow into the HCCI engine when the HCCI engine is operating in a first combustion mode, wherein the first plurality of estimates are based on an intake manifold absolute pressure (MAP), a mass air flow (MAF) rate, and a camshaft position. The sensor diagnostic module determines a state of at least one of a first plurality of sensors based on a predetermined threshold and differences between one of the first plurality of estimates and others of the first plurality of estimates, wherein the first plurality of sensors includes a MAP sensor, a MAF sensor, and a camshaft sensor.