This work deals with a finite element procedure developed to perform the eigenvalue analysis of damped gyroscopic systems, represented by flexible rotors supported on fluid film journal bearings. The rotor finite element model is based on the Timoshenko beam theory, accounting for the shaft rotary inertia and gyroscopic moments. The governing equations for the hydrodynamic journal bearing are obtained through the Galerkin weighted residual method applied to the classical Reynolds equation. A perturbation scheme on the fluid film governing equation permits to obtain the zero-th and first order lubrication equations for the bearings, which allow the computation of the dynamic force coefficients associated with the bearing stiffness and damping. The rotor-bearing system equation, which consists of a case of damped gyroscopic equation, is rewritten on state form to compute the complex eigenvalues. The natural frequencies at several operating conditions are obtained and compared to the technical literature data. The influence of the effective damping on the eigenvalue real part sign is analyzed for some examples of rotor-bearing systems, showing how the stability conditions can be predicted by the eigenvalue analysis. The procedure implemented in this work can provide useful guidelines and technical data about the selection of the more appropriate set of bearing parameters for rotating machines operating at stringent conditions.