DNA heteroduplex (HD) electrophoretic patterns of DQB1 alleles from 124 individuals (38 members from 7 families and 43 kidney donor-recipient pairs) were analyzed in reference to each individual's DQB1 diallelic types determined by the polymerase chain reaction-RFLP method. The assignment of DQB1 homozygosity and heterozygosity, based solely on HD patterns, was accurate and correlated well with the typing results. DQB1 homozygotes invariably gave HD patterns of a single band while heterozygotes gave HD patterns of multiple bands. Distinct HD patterns of 2 heterozygotes predict the presence of at least 1 different DQB1 type between the pair. However, pairs with identical HD patterns may have different subtypes, because HDs with 1 or 2 nucleotide differences may sometimes give an identical HD pattern. Because of its simplicity and reproducibility, this HD analysis protocol serves as an excellent alternative to screen for DQB1 homozygotes and mismatched tissue donor-recipient pairs. This protocol is also useful for confirming the correctness of DQB1 allelic type assignments in a clinical setting.