Buerger disease (BD) and Takayasu arteritis (TA) are rare vascular disorders. Although their etiology and pathogenesis have not been elucidated, several studies have suggested the involvement of innate immunity. Myeloid differentiation primary-response protein 88 (MyD88) is a key signaling adaptor for all Toll-like receptors, which have a central role in innate immunity. In the present study, we evaluated the association of MyD88 with BD and TA. We conducted case-control studies in Japanese populations composing of 131 BD cases, 90 TA cases and 270 healthy controls to be genotyped for a single nucleotide polymorphism rs7744 A>G in the 3'-untranslated region of MyD88 gene. The frequency of GG genotype was significantly lower in the BD patients than in the controls (6.9 vs 15.9%, P=0.011, odds ratio=0.39, 95% confidence interval; 0.19, 0.81), although there was no significant difference in the genotype frequencies between the TA patients and controls. It was suggested that MyD88 may confer resistance to BD in Japanese. Because this is the first report of the association between MyD88 and BD, replication studies in other cohorts are required.