BACKGROUND Intra-ampullary papillary-tubular neoplasm (IAPN) is recognized as a precancerous lesion with a great tendency to evolve into pancreatic cancer. The Surveillance, Epidemiology, and End Results (SEER) database is now large enough to study unusual cancers. Based on pathologic and epidemiologic characteristics of IAPN available in SEER, important clinicopathological correlations can be made. MATERIAL AND METHODS Cases of IAPN and other intraductal papillary mucinous neoplasms of the bile duct (OBIPMN) diagnosed between 1973 and 2014 were searched in the SEER database. The analysis was carried out with respect to patient clinical characteristics, tumor characteristics, incidence, and survival. RESULTS In total, 685 patients with IAPN were identified compared with 2465 patients with OBIPMN in the same period. The incidence rate of IAPN was decreased, with a 4.882% annual percent change. The patient characteristics of IAPN were quite different from OBIPMN in many characteristics, including age, gender, marital status, and survival. Compared with OBIPMN, the tumor characteristics of IAPN indicated that more patients were diagnosed at an earlier stage in multiple stage systems such as pathological grade (P<0.001), sixth American Joint Committee on Cancer stage (P<0.001), TNM stage (P<0.001), and SEER historic stage (P<0.001). In the survival analysis, the cancer-specific survival of IAPN was significantly better than OBIPMN (P<0.001) and the cancer-specific survival get worse at higher stages (P<0.001). Moreover, the 5-year cancer-specific survival rate of IAPN was also significantly better than that of OBIPMN (36.5% versus 25.4%, P<0.001). Finally, the multivariate analysis showed a correlation between cancer-specific survival and age of diagnosis and N stage (P<0.001). CONCLUSIONS Analysis of the SEER database clearly demonstrated that IAPN was a precancerous lesion tend to be diagnosed earlier compared with OBIPMN, which contributed to the better prognosis, and surgery was suggested if possible.