A method for controlling combustion in a multi-cylinder internal combustion engine operating in a controlled auto-ignition mode includes providing combustion control parameters, determining peak cylinder pressures and crank angle location of the peak cylinder pressures. Cylinder volumes at the peak cylinder pressures and at intake valve closings are determined and cylinder pressures at intake valve closings are determined. A combustion parameter for each cylinder is calculated based upon the peak cylinder pressure, the cylinder pressure at the intake valve closing, the crank angle location of the peak cylinder pressure, the cylinder volume coincident with the peak cylinder pressure, and the cylinder volume at the intake valve closing. A target combustion parameter is determined and the calculated combustion parameter for each cylinder is compared to the target combustion parameter. The provided combustion control parameters for each cylinder are adjusted to balance the combustion parameter across all cylinders based on the comparison. The engine is controlled based on the adjusted provided combustion control parameters.