Manufacturing/design imperfections and component failures in the fuel system/engine can lead to non-uniform torque production among the cylinders. Non-uniform cylinder torques can be observed as small engine speed fluctuations about the average engine speed at any given operating point. Severe imbalance conditions can be heard, felt, and seen by human operators. The present invention uses the fluctuations in engine speed to detect an unbalanced engine and attempts to correct the unbalance by applying trims to the fueling commands for each individual cylinder. The present invention is based on the calculation of a 6-point Fourier Transform (FFT) of engine speed data over one complete engine cycle. This FFT is calculated continuously to provide imbalance detection. An unbalanced engine results in non-zero magnitudes of the FFT components that correspond to the 0.5, 1.0, and 1.5 engine orders. The compensation scheme of the present invention uses iteration to drive the magnitudes of these components to zero if the engine is detected to be unbalanced.