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A rare case of cysts simultaneously occurring in the intrapancreatic accessory spleen and spleen in a 49-year-old female is reported. The patient underwent distal pancreatomy for a cystic tumor of the pancreas, and a splenectomy. A multilocular cyst (4.3 × 2.6 cm) in an accessory spleen at the pancreas tail, and a solitary cyst (1.2 × 0.9 cm) of the spleen were found. The cyst in the intrapancreatic accessory spleen was lined by non-keratinizing stratified squamous epithelium, and the spleen cyst by a single layer of flat epithelium; these lining cells were positive for Alcian blue stain and periodic acid-Schiff reaction, and were immunohistochemically positive for cytokeratin, HBME-1 and Sialyl-Tn. Epithelial membrane antigen, carcinoembryonic antigen and CA19-9 were positive in the accessory spleen cyst but were negative in the spleen cyst. An electron microscopic examination of the flat epithelium of the spleen cyst revealed numerous microvilli on the surface, cytoplasmic microfilaments, and a number of tight junctions between adjacent cells. These features suggested that the two cysts differ in nature, and origin; the accessory spleen cyst may be an embryonic inclusion of the pancreas duct while the spleen cyst may be an inclusion cyst of the mesothelium.