Non-transitional cell carcinomas (non-TCC) of the upper urinary tract as squamous cell carcinoma (SCC), adenocarcinoma, and small cell carcinoma (SmCC) are rare with few case reports in the literature. We retrospectively reviewed our patients who surgically treated for upper tract urothelial carcinoma from 1983 to 2013 for non-TCC pathological cancer characteristics and survival. Among 305 patients, only 5 (1.6%) cases were found: One case of SmCC, another had adenocarcinoma, and 3 SCC cases. None of them had intravesical recurrence and the cancer-specific survival for non-TCC cohort is markedly decreased (log-rank = 0.01) compared to TCC patients.