We describe a simple polymerase chain reaction (PCR)-based method for isolating short stretches of non-telomeric DNA adjacent to arrays of telomere repeat units, in principle applicable to any species for which the telomere repeat sequence is known. Application of this approach to human DNA resulted in the isolation of many candidate telomere junction clones, at least some of which were shown to be derived from telomere-adjacent regions. Most of the isolated clones detect multiple sequences in the human genome which represent one or a few sequence families present at the ends of most or all autosomes and variably truncated before the start of the telomere repeat array. Substantial sequence divergence between different members of these sequence families suggests a low rate of sequence homogenization by telomere exchange processes. The pseudoautosomal telomere junction has also been isolated and contains a shortened version of a recently described family of short interspersed repetitive elements (SINEs), only 14 base pairs (b.p.) from the start of the telomere.