The paper is dedicated to research on flexible rotor systems with anisotropic rotor material properties. In addition, the anisotropy of rotor supports alters the rotor system resonance frequencies and the machine has to pass till it attains the operating angular speed. This phenomenon of rotor vibration is observed in vertical rotors. The aim of this work is to compare experimental vibration measurements and results of theoretical modeling. In the paper theoretical model, created from physical one of really existing rotor system is described. Collected experimental data of rotor vibrations in bearings are compared with results of theoretically derived equations. The results of theoretical modeling and research enables for estimation of a more precise technical condition of the rotor system both after the overhaul and during the maintenance and thus to avoid unexpected breakdowns, especially concerning the fatigue development in ball bearing elements.