We investigate shear wave polarization in the Hayward fault zone near Niles Canyon, Fremont, CA. Waveforms of 12 earthquakes recorded by a seven-accelerometer seismic array around the fault are analysed to clarify directional site effects in the fault damage zone. The analysis is performed in the frequency domain through H/V spectral ratios with horizontal components rotated from 0° to 180°, and in the time domain using the eigenvectors and eigenvalues of the covariance matrix method employing three component records. The near-fault ground motion tends to be polarized in the horizontal plane. At two on-fault stations where the local strike is N160°, ground motion polarization is oriented N88 ± 19° and N83 ± 32°, respectively. At a third on-fault station, the motion is more complex with horizontal polarization varying in different frequency bands. However, a polarization of N86 ± 7°, similar to the results at the other two on-fault stations, is found in the frequency band 6–8 Hz. The predominantly high-angle polarization from the fault strike at the Hayward Fault is consistent with similar results at the Parkfield section of the San Andreas Fault and the Val d’Agri area (a Quaternary extensional basin) in Italy. In all these cases, comparisons of the observed polarization directions with models of fracture orientation based on the fault movement indicate that the dominant horizontal polarization is near-orthogonal to the orientation of the expected predominant cracking direction. The results help to develop improved connections between fault mechanics and near-fault ground motion.