Background: Intraductal papillary mucinous neoplasm (IPMN) of the pancreas is reported to have a high prevalence of extrapancreatic malignancy (EPM). The aims of this study were to evaluate the prevalence and associated factors of EPMs in IPMN patients and to compare these data with those of non-IPMN pancreatic cystic neoplasm (PCN) patients. Methods: The study included 385 PCN patients (210 IPMNs and 175 non-IPMNs) diagnosed from 1993 to 2007. PCN types, presence of EPMs, chronological relation of EPMs to PCN diagnosis, and their clinicopathological parameters were analyzed. Results: The prevalence of EPM was 33.8% for IPMNs and 12.0% for non-IPMN PCNs (P < 0.001). In the majority of patients with EPMs, PCNs were detected while undergoing workup for the EPMs. For IPMNs, age was associated with EPMs [odds ratio (OR) 1.05, P = 0.013]; malignant IPMN showed a borderline inverse association with EPMs (OR 0.50, P = 0.071). Multivariate analysis of entire PCN cohort demonstrated that age at PCN diagnosis (OR 1.05, P < 0.001) was positively associated with EPM; IPMN showed a borderline positive association with EPM (OR 1.88, P = 0.052). Malignant PCN (OR 0.40, P = 0.009) was inversely associated with EPM. Conclusion: The EPM prevalence of IPMN patients was 33.8%. Advanced age at IPMN diagnosis was the only factor significantly associated with EPMs in our IPMN cohort. In our PCN cohort, advanced age at PCN diagnosis was associated with malignant PCN and IPMN showed a borderline positive association with EPM.