A new balancing method for a flexible rotor bearing system with complex mode shapes was developed. In this method, a rotor system can be balanced at all the desired speeds and positions without trial runs. The balancing was obtained with the initially measured vibration signals at the speeds to be balanced and the calculated influence coefficients by complex modal analysis. It was proved that the result from the modal balancing of a flexible rotor with complex mode shapes is equivalent to that from so called influence coefficient method in certain conditions. A F.E.M. program was developed to calculate the influence coefficients by the complex modal analysis. In order to improve the reliability of the program, the structural parameters(bearing stiffness,damping,shaft stiffness etc.) were compared and tuned with the experimentally obtained parameters. Nevertheless,in the case the influence coefficients have some errors, they can be corrected by the comparison of the residual vibrations with the initial ones. The validity of this method was tested with an actual rotor system.