Mucinous cystic neoplasms and serous microcystic adenomas account for the majority of cystic tumors of pancreas. Mucinous cystic neoplasms and serous microcystic adenomas have different frequencies of progression to malignancy. The genetic and epigenetic alterations of these tumors have not been studied in detail. In this study, we compared methylation status of p16, p14, VHL, and ppENK genes by methylation-specific PCR (MSP), and genetic alterations including K-ras and beta-catenin gene mutations, chromosome 3p loss, and microsatellite instability in 15 mucinous cystic neoplasms (10 benign and 5 borderline) and 16 serous microcystic adenomas. There were no significant differences between mucinous cystic neoplasms and serous microcystic adenomas in methylation of p16 (14%, 2/14 and 12%, 2/16), p14 (15%, 2/13 and 37%, 6/16), VHL (0/14 and 7%, 1/14), and ppENK (0/14 and 0/13), respectively. K-ras mutation was present only in mucinous cystic neoplasms but not in serous microcystic adenomas (33%, 5/15 versus 0/16; P =.004). In addition, LOH at 3p25, the chromosomal location of VHL gene, was present in 57% (8/14) of serous microcystic adenomas compared with in 17% (2/12) of mucinous cystic neoplasms (P =.03). No beta-catenin mutation, microsatellite instability, or mutation of transforming growth factor beta type II receptor was present in either type of tumors. In conclusion, K-ras mutations and allelic loss of VHL locus at 3p25, but not methylation, distinguished mucinous cystic neoplasms and serous microcystic adenomas. The differences in genetic alterations but not epigenetic alterations may explain the pathogenesis and progression to malignancy of these cystic tumors of pancreas.