This work attempts experimental studies in finite element model updating of an actual rotor system mounted on ball bearings by using Inverse Eigen Sensitivity Method (IESM). The IESM is applied on state space representation of equations of motion and is used to identify bearing stiffness, damping and shaft material damping parameters. Non-proportional viscous damping model is used to model the bearing and shaft material damping. The experimental identification of viscous coefficient of shaft material damping was not found in the available literature and this work attempts the same as well. The updated model is validated for its accuracy by comparing the predicted frequency response with that obtained from the experiments. Finally, it is shown that the updated finite element model of the rotor system can be efficiently used to predict the unbalance in the rotor. (C) 2013 Elsevier Ltd. All rights reserved.