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This paper presents an effective analysis approach for a flexible rotor in ball bearings with nonlinear stiffness characteristics to obtain realistic dynamic behavior results. The ball bearing is modeled in five degrees of freedom and the nonlinear stiffness characteristics of the bearing are completely described as functions of combined loads and spin speed. For dynamic behavior analysis of the nonlinear rotor-bearing system, a transfer-matrix method is iteratively used until the bearing displacements and the shaft displacements at every bearing location converge to the same values. The results show that the nonlinear stiffness characteristics of ball bearings significantly influence system dynamic behaviors and the proposed analysis approach for the nonlinear rotor-bearing system is effective.