We report on three Japanese patients (two families) with familial Mediterranean fever (FMF), a rare disease in the Far East. Two of the patients (siblings with definite FMF) were heterozygous for both E148Q and M694I, and the remaining patient (with probable FMF and no family history of the disease) was heterozygous for both P369S and R408Q. Although the M694I mutation is less common among Mediterranean populations, it was present in 22 (76%) of 29 Japanese patients with FMF (previously reported cases). We therefore investigated the allele frequency of M694I in the healthy Japanese population, as well as other FMF-causing mutations in exon 10 (M680I, M694V, and V726A) and polymorphisms (E148Q, P369S, and R408Q) of the Mediterranean fever gene (MEFV). The allele frequencies of disease-causing mutations, even M694I, were <0.001. While those of E148Q, P369S, and R408Q were 0.23, 0.057, and 0.054, respectively. Because of the low allele frequencies of disease-causing mutations, FMF is an extremely rare disease among Japanese individuals. However, FMF is an important component of hereditary autoinflammatory syndrome, and a diagnosis of FMF is crucial for the choice of treatment, because of the benefit of colchicine therapy.