Mammalian sex chromosomes are divided into sex-specific and pseudoautosomal regions. Sequences in the pseudoautosomal region recombine between the sex chromosomes; the sex-specific sequences normally do not. The interface between sex-specific and pseudoautosomal sequences is the pseudoautosomal boundary. The boundary is the centromeric limit to recombination in the pseudoautosomal region. In man, an Alu repeat element is found inserted at the boundary on the Y chromosome. In the evolutionary comparison conducted here, the Alu repeat element is found at the Y boundary in great apes, but it is not found there in two Old World monkeys. During the evolution of the Old World monkey and great ape lineages, homology between the sex chromosomes was maintained by recombination in the sequences telomeric to the Alu insertion site. The Alu repeat element did not create the present-day boundary; instead, it inserted at the preexisting boundary after the Old World monkey and great ape lineages diverged.