The genetic loci conferring susceptibility to Graves' disease remain unclear. The aim of the present study was to examine a C/T polymorphism in the 5'-untranslated region of the CD40 gene and its relationship with autoimmune thyroid diseases in Koreans. The C/T polymorphism in the 5'-untranslated region of CD40 gene, clinical characteristics, and thyroid antibodies were analyzed in a series of Korean patients (132 with Graves' disease, 118 with Hashimoto's thyroiditis, and 164 normal controls). The CC genotype was significantly associated with Graves' disease (odds ratio, 1.93; 95% confidence interval, 1.21-3.09; corrected p = 0.019). On the other hand, the frequency of the TT genotype was significantly lower in Graves' patients than in controls (8% vs. 18%; odds ratio, 0.38; 95% confidence interval, 0.18-0.82; corrected p = 0.044). Allele frequencies in CD40 did not differ from controls in patients with Hashimoto's thyroiditis. In patients with Graves' disease, there were significant differences between genotypic groups in the activity of stimulating thyrotropin (TSH) receptor antibody. However, clinical characteristics and other thyroid antibodies were not significantly different. In conclusion, the C allele in the 5'-untranslated region of the CD40 gene may confer genetic susceptibility to Graves' disease in Koreans.