The paper deals with the analysis of shaft-rotor system which is under parallel misalignment. Misalignment is one of the most commonly observed faults in rotating machines. Misalignment is the second common mechanical fault in rotating machine applications after unbalance. The aim of the paper is to investigate the misalignment problem in rotating system using its vibration signature analysis. Parallel misalignment was given to the well aligned shaft-rotor system.Experimental studies were performed on a shaft-rotor system at to predict the misalignment in system. Analysis of shaft-rotor system with parallelmisalignment is done by using FFT (Fast Fourier Transform) analyser. In experimental results acceleration pick occurs which shows misalignment in system. Vibration analysis therefore helps to detect misalignment in the system.