INTRODUCTION: The purpose of this ex vivo study was to assess the effect of two root-end filling materials against Candida (C) Albicans. MATERIALS AND METHODS: ProRoot MTA and CEM Cement were compared immediately and 24 h after mixing, in two different concentrations (50 and 100 mg/mL). A total of 50 culture wells were used and divided into experimental (n=10) and control groups (n=5). Those with no medication served as positive and without C. Albicans served as negative controls. All plates were incubated at 37°C after 1, 24, and 48hours. At each interval, the presence of C. Albicans was assessed and recorded by an independent observer. In addition to observing turbidity, 0.02 mL of samples from each cell was re-cultured on sabouraud dextrose agar plates to confirm change in fungal growth. The data were evaluated and analyzed using Kruskal-Wallis test. RESULTS: Although all fresh and set samples with experimental concentrations showed fungal growth after 1 h; they demonstrated complete fungicidal activity at 24 and 48-h time intervals. CONCLUSION: Under the conditions of this ex vivo study, CEM cement as well as ProRoot MTA has fungicidal effects against C. Albicans even in concentration of 50 mg/mL and after 24 hours.