The effects of the incident wave polarization on the boresight error induced by the radome of a Ka-band monopulse antenna-radome system were analyzed. The boresight errors in the scanning space are determined by the ray tracing method. The results indicate that the in-plane boresight errors of the radome are independent on the incident wave polarization, the cross-plane boresight errors are less dependent on it, and the boresight errors in the scanning angles away from the azimuth and elevation planes are very sensitive to the incident wave polarization. The counter maps of the boresight errors with different incident wave polarization angles were also plotted and it shows that the boresight errors are rotating slowly with the change of the incident wave polarization.