DNA-restriction fragment length polymorphism (RFLP) typing is a well-established technique for routine identification of HLA-DR and -DQ allotypes. Methods and an interpretation scheme are presented which permit the identification of HLA-DR and -DQ allotypes using a single restriction endonuclease, TaqI. Resolution between problematic specificities may be rapidly achieved by simple polymerase chain reaction (PCR) based supplementary tests. Prior to hybridization, genomic DNA is treated by digestion with a restriction endonuclease; endonucleolytic fragments are then separated according to size by agarose gel electrophoresis and are transferred to a solid support by capillary or vacuum blotting. Although originally advocated as a technique with only a supplementary role in tissue typing, subsequent studies have shown that RFLP analysis permits the accurate genotyping of most DR, DQ, and Dw specificities. Major applications of RFLP analysis include the selection of DR/DQ-matched donors for allogeneic bone marrow transplantation, pretransplant typing of renal allograft recipients, and retrospective typing of cadaveric kidney donors.