The reconstructive surgery of urothelial defects, such as severe hypospadias is susceptible to complications. The major problem is the lack of suitable grafting materials. Therefore, finding alternative treatments such as reconstruction of urethra using tissue engineering is essential. The aim of this study was to compare the effects of naturally derived acellular human amniotic membrane (hAM) to synthetic poly-L-lactide-co-ε-caprolactone (PLCL) on human urothelial cell (hUC) viability, proliferation and urothelial differentiation level. The viability of cells was evaluated using live/dead staining and the proliferation was studied using WST-1 measurement. Cytokeratin (CK)7/8 and CK19 were used to confirm that the hUCs maintained their phenotype on different biomaterials. On the PLCL, the cell number significantly increased during the culturing period, in contrast to the hAM, where hUC proliferation was the weakest at 7 and 14 days. In addition, the majority of cells were viable and maintained their phenotype when cultured on PLCL and cell culture plastic, whereas on the hAM, the viability of hUCs decreased with time and the cells did not maintain their phenotype. The PLCL membranes supported the hUC proliferation significantly more than the hAM. These results revealed the significant potential of PLCL membranes in urothelial tissue engineering applications.