Pancreatic endocrine and/or exocrine functional disorders can be commonly detected in patients with inflammatory bowel diseases. Autoimmune pancreatitis is a rare disease and its co-existence with inflammatory bowel disease has been rarely reported. The diagnosis of autoimmune pancreatitis is difficult due to variable nonspecific symptoms, and the high rate of asymptomatic cases. The conventional imaging scans (ultrasonography, computed tomography, retrograde cholangiography) are usually not sensitive enough and they are frequently not able to differentiate between inflammatory and malignant tumorous diseases of the pancreas. The authors present the case history of a patient who developed both ulcerative colitis and autoimmune pancreatitis. The morphological changes of the pancreas detected by ultrasonography suggested the presence of pancreatic cancer, and this diagnosis was supported by the elevated level of serum CA19-9. Computed tomography failed to identify abnormalities in the pancreas and, finally, endoscopic ultrasound combined with fine needle aspiration cytology confirmed the diagnosis of autoimmune pancreatitis.