We investigated a possible association between Kawasaki disease (KD), a systemic vasculitis of unknown etiology, or its coronary artery lesions (CAL) and MEFV gene variants including E148Q, the most common and mild mutation in the MEFV gene for familial Mediterranean fever or vasculitis-related disorders. The study population comprised a total of 138 Japanese patients with KD, including 45 patients with CAL and 93 patients without CAL and 170 normal controls. Sequence variations for the MEFV gene were detected by direct sequencing, followed by the TaqMan SNP genotyping assay. The genotype and allele frequencies of MEFV gene variants (E148Q, L110P, R202Q, P369S, R408Q) were compared between KD patients with and without CAL or between KD patients with CAL and controls. E148Q heterozygotes and homozygotes were observed in 37.1 and 5.5% of healthy controls, 33.3 and 5.1% of KD patients, and 37.8 and 4.4% of KD patients with CAL. No significant differences were observed in the genotype and allele frequencies of other MEFV gene variants (L110P, R202Q, P369S, R408Q) between KD patients with and without CAL or between KD patients with CAL and controls. No associations were detected between the MEFV gene variants and the development of KD or CAL formation in KD.