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A known problem of the HCCI engine is its lack of direct control and its requirements of feedback control. Today there exists several different means to control an HCCI engine, such as dual fuels, variable valve actuation, inlet temperature and compression ratio. Independent of actuation method a sensor is needed. In this paper we perform closed-loop control based on two different sensors, pressure and ion current sensor. Results showing that they give similar control performance within their operating range are presented. Also a comparison of two methods of designing HCCI timing controller, manual tuning and model based design is presented. A PID controller is used as an example of a manually tuned controller. A Linear Quadratic Gaussian controller exemplifies model based controller design. The models used in the design were estimated using system identification methods. The system used in this paper performs control on cycle-to-cycle basis. This leads to fast and robust control.