Males with a Yq deletion are well described, but few have been studied with both cytogenetic and molecular techniques to define the deletion and relate it to the phenotype. This study reports an analysis of cells obtained from a college student with azoospermia, short stature, and a small penis. Cytogenetic analysis indicated that the entire Yq was deleted, but DNA hybridization showed that a portion of Yq12 remained. We conclude that the deletion is interstitial.