Isochromosomes for the long arm of the Y chromosome are rare and only a few cases have been reported in the literature. The isochromosome for the long arm of the Y chromosome serves as a unique opportunity for looking at factors relating to the genetic function of the Y chromosome. Localization of the gene(s) responsible for differentiation of the human gonad on either the long or short arm of the Y chromosome has been a long-standing question. This case is also pertinent to the reports of increased risks of gonadal tumors in gonadal dysgenesis patients with either a normal or abnormal Y chromosome present in their karyotype. Fibroblasts from this individual were determined to be H-Y antigen-negative. This evidence strongly suggests that the H-Y antigen gene is located on the short arm of the Y chromosome in man.