Deletions of specific regions on the Y chromosome cause male infertility. Recent advances in infertility treatment allow Y chromosome deletions to be transmitted to male offspring with the assumption that there will be no clinical consequences other than infertility in adult life. We screened 12 patients, who had a 45X/46XY karyotype and presented with Turner stigmata or sexual ambiguities, or both, for Y chromosome microdeletions with PCR. A third of these patients had Y chromosome microdeletions of distal Yq, the most common microdeletion seen in infertile men with azoospermia or severe oligozoospermia. Transmission of Y chromosome microdeletions could potentially have severe clinical consequences other than male infertility, such as the development of sexual ambiguities and Turner stigmata.