Deletions of the long arm of the Y chromosome have previously been associated with azoospermia and short stature. We report the results of a detailed clinical and molecular study of nine males with partial deletions of Yq. Special emphasis was laid on congenital anomalies and dysmorphic features. Some of the patients have developmental problems or distinct facial features, namely a small chin and mouth, a high arched or cleft palate, downward slanting palpebral fissures, high nasal bridge, and dysmorphic ears. As far as we know, similar facial dysmorphism has not been previously described in association with del(Yq). These features are not, however, simply correlated to the size of the deletion. In none of these patients could evidence of aberrant Xq-Yq interchange be found.