By using a turbo the operating range of the HCCI engine can be increased, but at the expense of increased controller complexity. The dynamics the turbo introduces in the intake and the exhaust manifolds, have a large impact on the in-cylinder mixture temperature, pressure and finally the combustion phasing. To compensate for this and to maintain desired combustion phasing, precise control of the negative valve overlap is required. A physical model is therefore developed and linearized to yield a state space model, used for Kalman filter and main feedback controller design. The original nonlinear model is inverted to provide feedforward. The main actuators for the controller are the intake and exhaust cam phasing, fuel amount and timing of the injections. The main sensor signals used by the controller are the cylinder pressure, intake exhaust pressure, and intake temperature. The model is validated against experimental data, simulated with the controller and finally the controller was tested on the real engine. The article shows the big picture of how a control system for a spray guided, turbo charged, negative valve overlap HCCI engine can be developed.