Complement C7 deficiency is associated with increased susceptibility to meningococcal infection. The genetic alterations of C7 deficiency are known to be sporadic and heterogeneous worldwide. We investigated molecular basis of C7 deficiency in two unrelated Korean families, in which the index cases suffered from meningococcal meningitis. Exon-specific PCR and direct sequencing of the C7 gene revealed two different mutations: c.1424G > A and c.281-1G > T. In family 1, index case and her brother revealed a homozygous mis-sense mutation (c.1424G > A), a novel mutation, which results in the change of cysteine to tyrosine (C475Y) in exon 10. Index case in family 2 was found to be a homozygote carrying point mutation at the 3' splice acceptor site of intron 3 (c.281-1G > T), which was previously reported in a Korean C7-deficient subject.