We compared the clinical features and long-term prognosis of 159 patients with type 1 autoimmune pancreatitis (AIP) with and without bile duct involvement. Eighty-nine (56%) patients had bile duct involvement. Forty-nine patients (30.8%) had relapse, with a significantly higher cumulative relapse rate in patients with stenosis or wall thickening upstream of the intrapancreatic bile duct (3 years: 24% vs. 37.1%, P<0.001). A significantly higher rate of two or more relapses (5.1% vs. 19.5%, P=0.01) was also found in these patients. Two patients with stenosis/dilatation up to the intrahepatic bile ducts became steroid-dependent and were treated with azathioprine. Type 1 AIP patients with stenosis and wall thickening upstream of the intrapancreatic bile ducts have a high relapse rate and may become steroid-dependent, especially in cases with stenosis and dilation extending into the intrahepatic bile ducts.