All human X-linked genes known so far, except for the Xp/Yp pseudoautosomal genes, are conserved as a single linkage group on the murine X chromosome. We show that the interleukin-9 (IL-9) receptor gene (IL9R), which is located within the human Xq/Yq homology region, maps to the murine chromosome 11. The Xq/Yq pseudoautosomal region (Xq PAR) thus represents a second region on the human X chromosome which is not X linked in mice. Furthermore, we show that IL9R is absent on the Y of great apes. IL9R is thus exceptional among X/Y genes in that it is X linked in some mammals, but autosomal or pseudoautosomal in others. Genes located on the X and the Y generally escape X inactivation. An exception to this rule is SYBL1, a gene located in Xq PAR. SYBL1 is X inactivated and is inactive on the Y chromosome. In contrast, we show that IL9R expression does occur from the Y, the active and the inactive X chromosomes. This finding raises the question of how the transcriptional regulation of genes within Xq PAR occurs and how the X inactivation status of IL9R has evolved following the autosome to X and the X to X/Y translocation. The evolutionary analysis of the IL9R gene, which is located at 10 kb from the telomere, and its pseudogenes at several telomeres, also provides insight into the evolution of these loci and of subtelomeric regions in general.