The dynamics and diagnostics of cracked rotor have been gaining importance in recent years. Relatively few authors have addressed the problem of multi crack assessment for rotors. In the present study a model-based method is proposed for the on-line identification of two cracks in a rotor. The fault-induced change of the rotor system is taken into account by equivalent loads in the mathematical model. The equivalent loads are virtual forces and moments acting on the linear undamaged system to generate a dynamic behaviour identical to the measured one of the damaged system. The rotor has been modelled using finite element method, while the cracks are considered through local flexibility changes. The cracks have been identified for their depths and locations on the shaft. The nature and symptoms of the fault, that is crack, are ascertained using the FFT.