We report a case of microcystic (glycogen-rich) adenoma of the whole pancreas with coexistent pancreatic low-grade malignant islet cell tumor in a 29-year-old woman. She complained of nausea, vomiting, and growing abdominal mass. Abdominal computed tomography showed multiple cysts in the whole pancreas and a calcified solid mass in the pancreatic head. A Whipple's operation and total pancreatectomy with splenectomy was performed to treat pancreatic cystic neoplasm. The pancreas was entirely replaced by variable-sized, multilocular cysts, which were lined by a flattened-to-cuboidal glycogen-rich epithelium. Furthermore, in the head of the pancreas, a focal yellowish solid mass showed a positive reaction for chromogranin A and neuron-specific enolase. Careful examination of the pancreas is warranted in cases of microcystic adenoma to rule out a possible coexistent pancreatic malignancy.