An autopsy case of chronic pancreatitis associated with unusual chronic thyroiditis in a 54-year-old woman is presented. Microscopically, the pancreas was densely infiltrated by lymphocytes and its exocrine parenchyma was completely replaced by sclerotic tissue. The thyroid gland was also infiltrated by lymphocytes, but no lymphoid follicles were observed. These morphological changes are rare findings with respect to the severity of inflammation and the association of the affected organs. Further findings suggested involvement of an autoimmune mechanism in the pathogenesis of these lesions. Using the avidin-biotin-conjugate technique and antibodies (Abs) against T lymphocyte and HLA-DR antigens (Ags), immunological aspects of the lesions were studied. Most of these infiltrating lymphocytes were revealed to be T lymphocytes, and HLA-DR Ags were observed on the epithelial cells of the pancreatic ducts and thyroid follicles. As a control, 45 surgical specimens of pancreas and thyroid gland were studied for detection of HLA-DR expression on the epithelial cells. One case of chronic pancreatitis was revealed to express HLA-DR Ag on the epithelium. The patient was a 44-year-old woman who had silently developed pancreatic cyst due to chronic inflammation. This finding also suggests a role of autoimmunity in the pathogenesis of chronic idiopathic pancreatitis.