In rotating machineries, misalignment is considered as the second most major cause of failure after unbalance. In this article, model-based multiple fault identification technique is presented to estimate speed-dependent coupling misalignment and bearing dynamic parameters in addition with speed independent residual unbalances. For brevity in analysis, a simple coupled rotor bearing system is considered and analytical approach is used to develop the identification algorithm. Equations of motion ingeneralized co-ordinates are derived with the help of Lagrange’s equation and least squares fitting approach is used to estimate the speed-dependent fault parameters. Present identification algorithm requires independent sets of forced response data which are generated with the help of different sets of trial unbalances. To avoid/suppress the ill-conditioning of regression equation, independent sets of forced response data are obtained by rotating the rotor in clock-wise and counter clock-wise directions, alternatively. Robustness of algorithm is checked for different levels of measurement noise.