Automotive requirement focuses on reducing misalignment that occurs in transmission systems. Due attention is given to the final gear drive including hypoid gear as it is easily susceptible to misalignment. It is significant to consider deviation in mounting position of gears along axial and angular directions to have reduced dynamic issues and smooth transmission. An alignment error between the gears contributes towards unbalanced force distribution. It is the major source of deviation from perfect conjugate gear drive. The paper focuses on identifying deflection that occur in Hypoid Gear having major application in Differential gear of automobile by considering the misalignment between them. Work done in this paper proposes new way to identify misalignment in hypoid gear using beam element modeling. With beams, it becomes easier to identify exact nature and deflection of gears from designed position. ANSA software is used as pre-processor. Maximum misalignment of 0.763 mm is found in Hypoid offset direction. The method is found to be in good agreement with analytical results for misalignments.