Several regions of sequence homology between the human X and Y chromosomes have been identified. These segments are thought to represent areas of these chromosomes that have engaged in ineiotic recombination in relatively recent evolutionary times. Normally, the X and Y chromosomes pair during mdosis and exchange DNA only within the pseudoautosomal region at the distal short arms of both chromosomes. However, it has been suggested that aberrant recombination involving other segments of high homology could be responsible for the production of X/Y translocations. We have studied four X/Y translocation patients using molecular probes detecting homologous sequences on X and Y chromosomes. In one translocation the breakpoints have been isolated and sequenced. The mapping data are consistent with the hypothesis that X/Y translocations arise by homologous recombination. The sequencing data from one translocation demonstrate this directly.The mammalian sex chromosomes are thought to have evolved from an ancestral homologous chromosome pair (1). Although sequences have been deleted, inserted, or rearranged on the sex chromosomes over time to accommodate their now specialized functions, significant sequence similarities remain between the present-day X and Y chromosomes. Sequences in the pseudoautosomal region at the terminal portions of the short arms of the sex chromosomes are identical and, during male meiosis, there is a single and obligatory X-Y crossover within this region (2). Occasionally the X-Y interchange occurs outside the pseudoautosomal region and the testis-determining factor (TDF) gene is transferred to the X chromosome resulting in an XX male phenotype (3, 4). Outside the pseudoautosomal region, homologous sequences have been found on the long arm of the X chromosome and the short arm or the proximal long arm of the Y chromosome. These regions share >95% similarity as detected by probes DXYS1, DXYS61, and others (5-10). Because some of these sequences are found only on the X chromosome of great apes, they are thought to have been generated by transposition of sequences from the X chromosome to the Y chromosome after the divergence of humans from great apes; however, recent loss of the Y homologs in great apes is also a possible explanation. In addition, several loci in the Xpter-Xp22 region were found to share 85-95% similarity with sequences in Yqll or the pericentric region of the Y chromosome. These include the genes for steroid sulfatase (STS; refs. 11 and 12), the tooth enamel protein amelogenin (AMG; ref. 13), and several loci defined by anonymous DNA fragments (14,15). The homology shared by the short arm of the X chromosome and the long arm of the Y chromosome has been cited as evidence for a pericen-