This paper presents the non-linear dynamic analysis of a flexible rotor having unbalanced and supported by ball bearings. The rolling element bearings are modeled as two degree of freedom elements where the kinematics of the rolling elements are taken into account, as well as the internal clearance and the Hertz contact non-linearity. In order to calculate the periodic response of this non-linear system, the harmonic balance method is used. This method is implemented with an exact condensation strategy to reduce the computational time. Moreover, the stability of the non-linear system is analyzed in the frequency-domain by a method based on a perturbation applied to the known harmonic solution in the time domain.