The Homogeneous Charge Compression Ignition (HCCI) combustion principle lacks direct ignition timing control, instead the auto-ignition depends on the operating condition and fast combustion phasing control is necessary for reliable operation. A six-cylinder heavy-duty HCCI engine was controlled on a cycle-to-cycle basis in real time using a variety of sensors, actuators and control structures for control of the HCCI combustion in comparison. Combustion phasing control based on ion current was compared to feedback control based on cylinder pressure. Two actuators were compared, dual fuel and Variable Valve Actuation (VVA). Model-based control synthesis requiring dynamic models of low complexity and HCCI combustion models were estimated by system identification and by physical modeling. The models identified by system identification were used to design model-predictive control (MPC) with several desirable features and today applicable to relatively fast systems. Both control of the combustion phasing and control of load-torque with simultaneous minimization of the fuel consumption and emissions were included.