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For internal combustion engines with electronic fuel-injection systems, differences in fuel injector performance may result in significant discrepancies between the fuel amounts injected into the individual cylinders. In order to avoid excessive torsional vibrations of the crankshaft due to nonuniform cylinder-wise torque contributions, it is important to calibrate the fuel injectors. This can be done using angular speed measurements of the crankshaft to reconstruct the gas torque applied on the flywheel and relating it to the cylinder firings. For engines with a high number of cylinders, an accurate engine model is essential for successful cylinder balancing. This is due to closely spaced cylinder firings and the fact that the crankshaft dynamics cannot be ignored, partly due to the increased length of the crankshaft, and partly because analysis of higher frequency components is required to obtain sufficient information for balancing the cylinder-wise torque contributions. The need for accurate models forms a major obstacle to the implementation of cylinder balancing methods for such engines. In this paper an online adaptive cylinder balancing method is proposed which can be applied to engines with unknown crankshaft dynamics. The procedure identifies the engine-specific phase-angle diagrams which relate the amplitudes and phases of the relevant torque frequencies to the cylinder firings. The identified model is applied to balance the cylinder-wise torque contributions of the engine with the objective of minimizing torsional vibrations. The proposed method is evaluated using both simulations on twelve and eighteen cylinder V-engine generator sets and experiments on a full-scale 6 MW six cylinder common-rail diesel power plant engine. The results show that the adaptive cylinder balancing procedure achieves a more efficient reduction of torsional vibrations than methods based on a fixed engine model, in which a rigid crankshaft is assumed.