Two polymorphic trinucleotide repeats of human androgen receptor gene (hAR), CAG and GGN which encode glutamine and glycine, have been shown to be associated with human diseases. The number of repeats ranges from 8 to 35 for the CAG and from 10 to 30 for the GGN in human populations. Longer CAG repeats are associated with reduced hAR transcriptional activity, spinal bulbar muscular atrophy and lower cognitive function in older men, whereas shorter CAG repeats are associated with increased risk of prostate cancer and infertility in men. The functional roles of the CAG and GGN repeats have not been clarified. In order to compare the sequence of the CAG and GGN regions in apes, we analyzed 57 chimpanzees, 18 gorillas, 20 orangutans, 16 agile gibbons, and 17 siamangs by PCR and electrophoresis. Two bonobos and one long-tailed macaque were also sequenced and the sequences of all species were aligned, respectively, with one human registered sequence. Seventeen different alleles (4, 7, 8, 9, 12, 14, 15, and 17-26 repeats) and 11 alleles (11-14 and 16-22 repeats) were detected at the CAG and the GGN loci, respectively. Although the repeat tract was conserved among apes, chimpanzees had alleles with a wide range of repeat lengths: (CAG)(14-26) and (GGN)(14-22). Gorillas were less polymorphic with the (CAG)(8) and (GGN)(19) alleles being most common, and orangutans exhibited monomorphic (CAG)(11) and (GGN)(22) alleles. On the other hand, agile gibbons and siamangs had the shortest (CAG)(4) allele, but showed variable length of GGN repeats (11-13 in agile gibbons and 16-21 in siamangs). In chimpanzees, frequent haplotypes consisting of short CAG repeats and long GGN repeats or vice versa was observed as in humans.