The author reports a rare autopsy case of primary small cell carcinoma of the urinary bladder with an emphasis on KIT and platelet-derived growth factor receptor-alpha (PDGFRA) genes. An 81-year-old man was admitted to Shizuoka City Shimizu Hospital because of dysuria. Cytology of the urine showed small carcinoma cells. Transurethral bladder tumorectomy indicated small cell carcinoma, and the patient was treated by radiation and chemotherapy. The patient died, however, of systemic metastasis 2 months after the first presentation. An autopsy showed a bladder small cell carcinoma and it systemic metastasis. Immunohistochemistry of the tumorectomy and autopsy specimens was positive for cytokeratins, neuron-specific enolase, synaptophysin, CD56, KIT and PDGFRA, and negative for chromogranin and thyroid transcriptional factor-1. Polymerase chain reaction-direct sequencing showed no mutations of KIT (exons 9, 11, 13 and 17) or PDGFRA (exons 12 and 18) genes in the tumorectomy specimens and was non-contributory due to DNA damage in autopsy specimens. The present case is the first case of primary small cell carcinoma of the urinary bladder involving examination of KIT and PDGFRA expression and KIT and PDGFRA gene mutations.