Differential DNA heteroduplex patterns were used to investigate inheritance of HLA class II region genes in a family where a living related kidney transplant was under consideration. Serologic typing of the family members for HLA class I (HLA-A, B, and C) and class II (HLA-DR and DQ) alleles indicated that the patient (109) and one sibling (126) had inherited the same maternal and paternal HLA alleles. However, a strong reciprocal mixed lymphocyte response implied that these two individuals were not completely HLA identical. Serologic typing for HLA-DQ was confirmed by allele-specific oligonucleotide typing family members for HLA-DQ alpha and beta genes. To assess a possible nonidentical gene(s), DNA was amplified from all family members at the second exon of the DR beta, DQ alpha, DP alpha, and DP beta genes and the products were analyzed by DNA heteroduplex formation. This method showed that individuals 109 and 126 were identical at DR and DQ but differed at DP. This difference was confirmed by allele-specific oligonucleotide hybridization and indicated that 126 had inherited a recombinant maternal chromosome with a cross-over occurring in the region between the DQ beta and DP alpha genes. These data demonstrate the applicability of DNA heteroduplex patterns in establishing identity-nonidentity of alleles in the major histocompatibility complex.