The probe 29C1 detects a hypervariable locus 18kb from the telomere of the human X and Y chromosomes, in the pseudoautosomal region. Here we report that hypervariability of fragments containing this sequence in the human population arises by loss or gain of a 31 base pair GC rich repeat. Labelled 29C1 does not detect a DNA fingerprint at low stringency, though the consensus repeat sequence does show some similarity to previously reported minisatellites. Sequence within the repeat block has G and C rich strands, a feature associated with sequences at the telomeres of many higher organisms. The repeat block shows sequence characteristics normally associated with a low methylation island, though the locus is methylated and does not appear to be transcribed.