The author reports a rare case of primary large cystic extragastrointestinal stromal tumor (eGIST) of the transverse mesocolon with genetic analyses of the c-kit and platelet-derived growth factor receptor-alpha (PDGFRA) genes. A 78-year-old man was found to have a large cystic tumor in the abdomen, and the tumor was resected. Grossly, the tumor was located in the transverse mesocolon, and cystic. Microscopically, the tumor consisted of epithelioid cells with atypia. Mitotic figures were noted in five of 50 high power fields. Immunohistochemically, the tumor cells were positive for KIT, CD34, PDGFRA, and vimentin, but negative for cytokeratins, neuron specific enolase, desmin, S100 protein, alpha-smooth muscle actin, p53 protein, HMB45, CD68, CEA, factor VIII-related antigen, chromogranin, and synaptophysin. Ki67 labeling was 5%. Genetically, the tumor showed a point mutation (GAC --> GTC) at codon 842 of exon 18 of the PDGFRA gene. Exon 12 of the PDGFRA gene and exons 9, 11, 13, and 17 of the c-kit gene showed no mutations. No recurrence is noted 3 years after the operation. This case shows that eGIST may occur in the transverse mesocolon.