We have developed a simple and efficient procedure with which to form single-stranded DNA (ssDNA) and then applied HLA-DRB1, -DQB1, and -DPBI allele typing. This method is referred to as low ionic strength single-stranded conformation polymorphism {LIS--SSCP), and is based on the diversity in the electrophoretic mobility of ssDNA formed by heat denaturation in low ionic strength solutions. This method detected DNA polymorphisms, including point mutations at a variety of positions in the DNA fragments of the HLA-DRBI, -DC2BI, and -DPB1 genes. Under our experimental conditions, stable ssDNA could be kept at room temperature ~S hr without having been cooled on ice immediately after heat denaturation. A total of 41 HLA-DRB1, 14 HLA-DQBI, and 17 HLA-DPBI alleles from 220 healthy people were analyzed using a combination of PCR-LIS-SSCP with group-specific amplification. All of the alleles analyzed were discriminated among the DRBI, DQB1, and DPBI groups except for DPBI*0402 and 020L The efficiency of ssDNA formation using the LIS-SSCP procedure was higher than that of the traditional formamide method, and the SSCP profiles were clearer than those of the original SSCP. This procedure is useful for screening new alleles as well as the donor-recipient molecular matching of HLA class !! genes, it is simple, rapid, and cost effective, requiring neither radioisotopes nor enzymes to confirm the typing results of other methods.The HLA class II (HLA-DR, -DQ, and-DP) antigens are heterodimers (cz and 13 chains) of highly polymorphic glycoproteins expressed on the surface of antigen-presenting cells and they play a key role in the immune recognition of foreign antigens (Zinkemagel and Doherty 1974;Babbit et al. 1985;Bach 1985;Schwartz 1985;Buus et al. 1987;Guillet et al. 1987;Stern et al. 1994). Allologous HLA class II antigens are also recognized by the immune surveillance system in tissue transplantation (Bach and Sachs 1987). The 13 chains of HLA-DR, -DQ, and -DP antigens show remarkable polymorphism in the first domain, and they are encoded by the second exon of the HLA-DRB, -DQB, and -DPB genes, respectively. HLA-DRB1, -DQB1, and -DPB1 have been reported to possess 124, 25, and 62 alleles, respectively (Bodmer et al. 1995).HLA class II DNA typing has become very ira- portant in the fields of basic and clinical medicine as HLA disease association and donorrecipient matching for transplantations increase. In heterologous bone marrow transplantation, HLA alleles must be typed with precision and efficiency for selecting the most appropriate donor. There are many methods of HLA allele typing. However, all of them have advantages and weaknesses, so at present, there is no perfect method that is easy, accurate, prompt, and cost effective. Single-stranded conformation polymorphism (SSCP) was developed by Orita et al. (1989) as a means of detecting a mutated sequence. This method is based on the fact that the electrophoretic mobility of a single-stranded nucleic acid in a nondenaturing polyacrylamide gel depends not only on its size...