Using a combination of in situ mapping and DNA analysis with recombinant DNA probes specific for the Sxr region of the mouse Y chromosome, we show that both the gene(s) controlling sex determination and the expression of the male-specific antigen H-Y (Tdy and Hya, respectively) are located on the minute short arm of the mouse Y chromosome. We demonstrate that the H-Y- variant of Sxr (Sxr') arose by a partial deletion within the Sxr region. Also, we show that intrachromosomal recombination between the Y short arm and Sxr' can sometimes occur during male meiosis, restoring the deleted DNA sequences and resulting in an H-Y+ mouse (male 719 in this paper). Based on these results, we propose a model for the generation of the original Sxr region and the Sxr' and Sxr719 variants.