We have developed a system for revealing informative and useful haplotypes for the human Y chromosome using PCR. Variant alphoid satellite DNA subunits were amplified and analysed by digestion with HindIII to score a restriction site polymorphism, or on polyacrylamide gels to reveal 13 heteroduplex haplotypes. Heteroduplexes are double-stranded DNA molecules containing mismatches; the haplotype is the combination of alleles on the same chromosome. Structural studies showed that the heteroduplexes analysed here were formed from loci at the left (short arm) and right (long arm) edges of the centromeric alphoid array which differed by a 4-bp insertion/deletion and several point mutations. Consequently, many haplotypes may have arisen only once and are useful for evolutionary studies.