Molecular studies are ongoing in regards to superficial urothelial carcinoma of the bladder (UCB) either to define targeted therapy or to better select aggressive therapy candidates and also to delineate the outcome of the disease. In this study, we aimed to present the impact of ALDH1 and CD44 as stem cell markers in tumorigenesis and their prognostic value in urothelial carcinoma. We investigated ALDH1 and CD44 immunohistochemically in paraffin-embedded material of 125 non-muscle-invasive (NMI) cases in 163 UCB patients. In the NMI-UCB subgroup, we found ALDH1 to be significantly correlated with all poor prognostic factors, including high stage (>= pT2), high grade, recurrence and progression development and poor survey (P=0.001) in contrast to CD44 expression (P>0.05). Although ALDH1 expression had a good correlation with a poor clinical course of UCB, it could be used as a molecular marker to determine the best treatment strategy and could contribute to the development of targeted therapies.