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Homogeneous charge compression ignition (HCCI) is one of the most promising piston-engine concepts for the future, providing significantly improved efficiency and emissions characteristics relative to current technologies. This paper presents a framework for controlling an HCCI engine with exhaust recompression and direct injection of fuel into the cylinder. A physical model is used to describe the HCCI process, with the model states being closely linked to the thermodynamic state of the cylinder constituents. Separability between the effects of the control inputs on the desired outputs provides an opportunity to develop a simple linear control scheme, where the fuel is used to control the work output and the valve timings are used to control the phasing of combustion. The controller is tested on both a single and multi-cylinder HCCI engine, demonstrating the value of a physical model-based control approach that allows an easy porting of the control structure from one engine to another. Experimental results show good tracking of both the work output and combustion phasing over a wide operating region on both engines. In addition, the controller is able to balance out differences between cylinders on the multi-cylinder engine testbed, and reduce the cycle-to-cycle variability of combustion.