Objective While the long-term prognosis of autoimmune pancreatitis remains unclear, diagnosis of various malignant neoplasms has been reported in several autoimmune pancreatitis case studies. We retrospectively investigated the relationship between type 1 autoimmune pancreatitis and the occurrence of malignant neoplasms. Methods Seventy-eight type 1 autoimmune pancreatitis patients were the subjects of this study. We investigated their clinical profiles, incidence of malignancies, and possible risk factors for developing malignancies, including duration of autoimmune pancreatitis, diabetes mellitus, and steroid therapy. Results Twelve patients developed malignancies after the diagnosis of autoimmune pancreatitis: colon cancer in five patients, lung cancer, pancreatic cancer and gastric cancer in two patients each, and hepatocellular cancer in one patient. In seven of the 12 patients (58.3%) a malignancy was detected within one year after the diagnosis of autoimmune pancreatitis. There were significant differences in gender, median age, and diffuse type of pancreas swelling between the group of patients with malignancies and the group without malignancies, but steroid therapy and diabetes mellitus were unrelated to the occurrence of malignancies in autoimmune pancreatitis. Conclusion The incidence of colon cancer in the type 1 autoimmune pancreatitis patients was higher than the incidence of other malignancies. Male, advanced age, and diffuse type of pancreatic swelling may be risk factors for malignancy in patients with type 1 autoimmune pancreatitis. It is recommended that male autoimmune pancreatitis patients over 70 years old who have been diagnosed with autoimmune pancreatitis within the previous year be examined for malignancy by a combination of gastrointestinal endoscopy, either chest X-ray or computed tomography scan, and abdominal ultrasound.