A modified transmission error (TE) model is introduced for analysing the effects on the transmission error of variation of tooth body stiffness with load application point, and a simulation program for transmission error computation with varying stiffness has been developed. In order to obtain the case where the tooth deflection component is the dominant source of the TE, nylon gears were used in this study. All the simulation results have been compared with the measured transmission errors from a single-stage gearbox. Even though carried out on low precision gears, the validity of the model for the more flexible nylon gears indicates that the model can be used for analysing the transmission error of high-precision gear sets.