We analyzed the single nucleotide polymorphisms (SNPs) in the sixth (C6) and the seventh (C7) component genes of the complement system in a sample of the Japanese population, using polymerase chain reaction (PCR)-based methods and PCR direct sequencing. SNPs in the C6 gene studied here are as follows: A413C in exon 3, T1674C in exon 10, T7145A in exon 13, G[357+32]A in intron 2, and G[503-78]A in intron 3. We confirmed that nt413A and nt413C were associated with C6A and C6B, respectively. The result of the nt2145 typing showed that two subtypes exist in the C6B allotype. The SNP of G[357+32]A in intron 2 could be analyzed by using the PCR-RFLP method with HinfI. Allele frequencies in the Japanese population were found to be *G=0.920 and *A=0.080. SNPs in the C7 gene are as follows: T382C in exon 4, G1166C and A1258C in exon 9, and G[+10]A in intron 13. Nt382C and nt1258C would be responsible for C7-5 (=C7-3) and C7-4 allotypes, respectively.