Many papers are available in the literature about identification of faults in rotor systems. However, they generally deal only with a single fault, usually an unbalance. Instead, in real machines, the case of multiple faults is quite common: the simultaneous presence of a bow (due to several different causes) and an unbalance or a coupling misalignment occurs often in rotor systems. In this paper, a model-based identification method for multiple faults is presented. The method requires the definition of the models of the elements that compose the system, i.e., the rotor, the bearings and the foundation, as well as the models of the faults, which can be represented by harmonic components of equivalent force or moment systems. The identification of multiple faults is made by a least-squares fitting approach in the frequency domain, by means of the minimization of a multi-dimensional residual between the vibrations in some measuring planes on the machine and the calculated vibrations due to the acting faults. Some numerical applications are reported for two simultaneous faults and some experimental results obtained on a test-rig are used to validate the identification procedure. The accuracy and limits of the proposed procedure have been evaluated.