Interferon therapy, widely used in chronic viral hepatitis and in various malignant diseases, has been known to induce autoimmune phenomena, the most frequent being autoimmune thyroid disease. We have studied the human leukocyte antigen (HLA) in patients who developed autoimmune thyroid dysfunction after interferon-alpha therapy for chronic hepatitis C. Seventeen of 439 patients (3.9%) developed symptomatic autoimmune thyroid dysfunction after interferon-alpha therapy, including nine cases of hyperthyroidism and eight cases of hypothyroidism. The incidence of HLA-A2 in those patients was significantly higher than that in general population in Japan. The present results suggest that HLA-A2 is associated with interferon-alpha therapy-induced autoimmune thyroid dysfunction in patients with chronic hepatitis C.