Transmission error is highly related to gear noise. In order to predict the helical gear noise, transmission error analysis is needed. Up to now, the studies for the transmission error were conducted by the modeling of helical gears only. However, since helical gears are supported by the shaft and bearing, transmission error has the effects of the elements. In this study, the procedure to consider the shaft deformation with bearing stiffness for the transmission error analysis is proposed. To do so, the relationship between gear error and shaft deformation is analytically derived. Shaft deformation with bearing stiffness is analyzed by FEM. It is measured in the experimental test rig by the non-contact displacement sensors. Using the tooth error from tooth modification and the shaft deformation, the effects of shaft on the loaded transmission error are investigated.