Presented is a case report of a urinary bladder carcinoma that had an unusual morphology and phenotype. A 65-year-old Japanese man complained of gross hematuria. Cytological examination of the urine before a partial cystectomy revealed small, round atypical cells with a high nuclear/cytoplasmic ratio, scant cytoplasm, and hyperchromatic nuclei with coarse and granular chromatin in a bloody background. Several tumor cells had relatively large and vesicular nuclei with prominent eosinophilic nucleoli and obscure perinucleolar halos. A small number of large atypical urothelial cells were also recognized. The tumor recurred locally 3 months after the operation. The urine cytology during recurrence showed the same features without the atypical urothelial cells. These cytological findings suggested a case of small cell undifferentiated carcinoma (SCUC) combined with transitional cell carcinoma (TCC). An histology of the resected specimen before the recurrence revealed that the SCUC was consistent with a variant type of SCUC proposed for the lung and showed transition with TCC in situ. M-VAC chemotherapy after a total cystectomy was less effective. The patient died 6 months after diagnosis. A variant subtype of SCUC of the urinary bladder associated with TCC in situ has not been previously reported. Although this histological type is very rare, its earlier cytological detection is needed for appropriate therapy.