IgG4-related disease has been identified in various organs, but whether or not there are organ-specific characteristics related to the etiologic factors is still unknown. Here, we carried out a cross-sectional study of 114 patients with IgG4-related disease. On the basis of the location of the lesions, the patients were classified into 5 groups: head and neck (n=23), thoracic (n=16), hepatic and pancreatobiliary (n=27), retroperitoneal (n=13), and systemic (n=35). All groups had similar clinicopathologic features in various aspects. However, there were some organ-specific features: for example, the proportion of the female patients was significantly higher in the head and neck group, serum IgG4 concentrations were significantly higher in the head/neck and systemic groups, and all kidney lesions were associated with extrarenal disease. Unique pathologic features were dense fibrosis in dacryoadenitis, numerous lymph follicles in sialadenitis and dacryoadenitis, and obliterative arteritis in lung lesions. In addition, an epithelioid granuloma and rheumatoid nodule were noted within IgG4-related lesions in 2 patients, 1 each with a history of tuberculosis and rheumatoid arthritis, respectively. Malignant tumors (2 lung cancers and 1 malignant lymphoma) were identified after the diagnosis of IgG4-related disease in 3 patients, all in the systemic group. In conclusion, this study showed organ-specific features of IgG4-related disease. Further study is necessary to conclude whether these features reflect different manifestations of a single disease entity or suggest different underlying etiologic factors.