The shaft misalignment, even being a common fault in rotating machinery, is not sufficiently studied. The present work addresses effects of misalignment in rotating machinery. An attempt to give a theoretical model for a rotor-coupling-bearing system has been done. The rotor-bearing system including the flexible coupling is modelled using the finite elements. The reaction forces and moments developed due to flexible coupling misalignment both for parallel and angular are derived and introduced in the model. Vibration analyses such as eigen value analysis and unbalance response are carried out for the rotor system with misaligned shafts.