Previous work has demonstrated discontinuous length variation at the tip of the short arm of human chromosome 16 (16pter) due to polymorphism of the subtelomeric region. We have now analyzed the zone where the two most common subtelomeric alleles (A and B) diverge. This lies 145 kb distal to the alpha-globin genes and comprises a complex segment of approximately 4 kb where there is partial loss of homology between the alleles, preceding the final point of divergence. Most notably, there is an imperfect (CA)n repeat that differs in length with different 16pter alleles and is exceptionally large (n = 250-350) in the case of the A allele and homologous sequences on Xqter and Yqter. Both the (CA)n expansion and the genetic exchange between chromosomes 16, X, and Y seem to have occurred since the divergence of man from other great apes. The occurrence of long (CA)n tracts may be related to the biology of subtelomeric regions.