A new and potentially reliable method for the isolation of yeast artificial chromosome (YAC)-insert termini, termed junction trapping, is described. This method is based on simple partial digestions of the YAC-containing yeast strain, ligation to a plasmid vector, and selection of the termini by two rounds of polymerase chain reaction (PCR). To date, the method has generated both terminal sequences from each of nine YACs (100%) that have been examined.