A multi cylinder homogeneous charge compression ignition engine includes actuators and an engine controller configured to reduce variations in combustion phasing and/or combustion energy release among the different engine cylinders. By sensing both the phasing and magnitude of the combustion energy release, the engine controller generates control signals to combustion phase controllers and combustion energy release controllers for the engine cylinders. The control signals may be different from one another to reduce variations across the group of engine cylinders. A combustion energy release controller may be a direct injection fuel injector, and the combustion phase controller may be a variable intake valve actuator. Reducing variations in these aspects of the combustion events, allows the engine to operate at higher speeds and loads.