A genotyping system for HLA‐Cw alleles using methods of PCR‐single‐strand conformation polymorphism (SSCP) and PCR‐sequence‐specific primers (SSP) was developed. Genomic DNA from 167 random healthy Japanese individuals were investigated to determine HLA‐C allele frequencies and their associations with HLA‐A and ‐B loci. Nine alleles were frequently detected: Cw*0102 (18.3%), Cw*0304 (12.0%), Cw*1202 (11.4%), CW*0303 (10.5%), Cw*1403 (10.5%), Cw*0801 (10.2%), Cw*0702 (9.0%), Cw*1402 (6.0%) and Cw*0401 (5.1%). Several HLA‐C‐B haplotypes such as Cw*0303‐B62, Cw*0304‐B60, Cw*0501‐B44, Cw*0602‐B13, Cw*0602‐B37, Cw*0702‐B7, CW*1202‐B52, Cw*1402‐B51 and Cw*1502‐B51 were found to be shared by Japanese and Caucasians. With the PCR‐SSCP method we could detect differences in each exon of HLA‐C alleles, at a low cost and simply. This method is suitable for sequence‐level matching with a relatively small number of samples.