An identification algorithm for the simultaneous identification of the bearing and unbalance parameters for flexible rotor-bearing systems has been developed by using run-down measurements. Speed-dependent bearing dynamic coefficients for each bearing and residual unbalances at predefined balancing planes are estimated simultaneously by the algorithm. The proposed identification algorithm is demonstrated through a numerical model. The identification procedure is found to be highly ill-conditioned and the Tikhonov regularization is applied to deal with this problem.