Autoimmune pancreatitis is a unique disease, characterized by lymphoplasmacytic inflammation in the acute stages. However, the active clinical features are unlikely to persist for longer periods. Through long-term follow-up, we investigated the disease course in 51 patients with autoimmune pancreatitis. We found recurrence in 21 (41%) and pancreatic stone formation in 9 (18%) patients. Pancreatic stone formation was significantly more frequent in the recurrence group (7/21; 33%), compared to the non-recurrence group (2/30; 7%). Moreover, we found high serum immunoglobulin-G4 concentrations in 13 of 175 (7.4%) patients with ordinary chronic pancreatitis. This suggested that pancreatic stone formation was closely associated with recurrence and that autoimmune pancreatitis may transform into ordinary chronic pancreatitis after several recurrences. We found that the immune complex level, with a cut-off value of 10 mg/dl, served as a good predictor of recurrence, with high sensitivity (61.9%), specificity (70.0%) and efficacy (66.7%). We also confirmed that human leukocyte antigen and cytotoxic T-lymphocyte antigen-4 polymorphism were useful predictors for autoimmune pancreatitis recurrence.3