Purpose Because nontransitional cell carcinoma neoplasms of the urinary tract are rare in Western countries, we examined the association between urinary cytology and pathology evaluations for these tumors. Materials and Methods An institutional review board approved, retrospective review of a total of 55,946 cytology evaluations in 12,705 patients between 1992 and 2004 was performed for correlation with subsequent histopathology findings. Documented urothelial neoplasms were then correlated with previous cytology results. Nontransitional cell carcinomas were categorized as adenocarcinoma, squamous cell carcinoma and other, including small cell disease, sarcoma, melanoma or lymphoma. Results All 108 patients with cytology evaluations showing adenocarcinoma had histological evidence of cancer and 86% had adenocarcinoma in the urinary tract. All 110 patients with squamous cell carcinoma on cytology had cancer, including 47% with primary squamous cell disease. All 42 patients with other nontransitional cell carcinomas on cytology evaluation had cancer, of whom 64% had histological concordance. In a separate analysis of 70 patients who had pathologically confirmed adenocarcinoma 57% had positive prior cytology findings, of whom 19% had histological concordance. Of 85 patients with squamous cell carcinoma 81% had positive prior cytology findings, of whom 60% had histological concordance. Of 83 patients with other nontransitional cell carcinomas 70% had positive prior cytology findings, of whom 31% had histological concordance. Conclusions In our series all patients with nontransitional cell carcinoma cytological results had cancer in the urinary tract. Thus, nontransitional cell carcinoma cytology findings mandate careful urinary tract evaluation. Concordance with histological subclassification on subsequent pathology evaluation ranges from 49% for squamous cell carcinoma to 86% for adenocarcinoma. A majority of patients with nontransitional cell carcinoma malignancies had positive prior cytology findings. However, the concordance with histological subclassification on prior cytology results ranges from 19% for adenocarcinoma to 60% for squamous cell carcinoma.