Sixty-five living related kidney transplant pairs were analyzed for matching at HLA class II loci by the polymerase chain reaction (PCR)--sequence specific oligonucleotide probe (SSOP) method. The retrospective HLA matching study revealed that there were many early graft loss cases despite the DQB compatibility, contrary to our expectation. There were 54 DRB1 one-mismatched cases, in which 7 of the 11 (64%) DQB zero-mismatched cases had lost their grafts, while the graft loss cases were only 10 of the 43 (23%) DQB one-mismatched pairs (P value = 0.0006). The DQB matching of these cases was studied in detail, because the PCR-SSOP methods are based on the detection of sequence polymorphisms in a relatively narrow range, i.e., recognized sequences by SSOPs. The PCR--heteroduplex--polymorphism analysis method was developed to analyze the polymorphism in exon 2 of the DQB1 gene. However, all the pairs proved to be compatible for the DQB, demonstrating that the DQB compatibility was associated with a harmful influence on the graft outcome. These observations suggested that the DQB1 incompatibility might exert the low responsiveness to HLA haplo-identical allogeneic transplants.