Background: Urothelial carcinomas (UC) can be either in the upper or in the lower urinary tract or both.  Urothelial bladder cancer (UBC) is more common than upper tract urothelial carcinoma (UTUC). This research was designed to study the biochemical difference between UBC and UTUC through the comparison between Catalase and Nitric oxide and the measurements of CK20 and CD44 by flow cytometry. Methods: To study the discrepancy between UBC and UTUC. A prospective trial was carried out for 28 radical cystectomy and 18 nephrouretrectomy specimens of UBC and UTUC patients, respectively.  The activity of Catalase and concentration of Nitric oxide were assessed in in normal adjacent tissues, UTUC and UBC spectrophotometrically. CK20 and CD44 also were assessed in in normal adjacent tissues, UTUC and UBC by flow cytometry. Results: Comparison between UBC and UTUC regarding Catalase had significant difference (P value < 0.05) and comparison between UTUC and UBC regarding nitric oxide had significant difference (P value < 0.05), regarding CK20 in UTUC was positive (73.6%) and in UBC was positive CK20 (62.4%) and regarding CD44 in UTUC was positive (65.5%) and in UBC was negative CD44 (52.2%). Conclusions: Even though UTUC and UBC have the same origin, there is clear evidence that there is a biochemical difference between them. This biochemical difference could be the reason that UTUC is more aggressive than UBC