Introduction: Root-end filling materials used in endodontic surgeries should maintain an adequate seal and prevent apical microleakage. The aim of this study was to compare apical microleakage between two new endodontic cements as root-end filling materials and MTA Angelus using fluid filtration system. Materials and methods: A total of 65 extracted single-rooted human anterior teeth were selected in this study. Canal preparation was carried out manually by step-back technique, following which the canals were obturated. The samples were divided into three experimental groups, each containing 19 samples, and two control groups, including four positive and four negative samples. The apical end of each root was resected, root-end preparation was done, and canals were filled with Calcium Aluminate α-Aluminate Cement (CAAC), a mixture of Wollastonite and CAAC (WOLCA), and MTA Angelus. Then, the samples were placed in the fluid filtration system to measure the amount of microleakage. Data were analyzed by SPSS (Version 19) using Analysis of Variance (ANOVA). P-values < 0.05 were considered significant. Results: Mean microleakage at all times was lowest in MTA Angelus and highest in CAAC cement. There was no significant difference between MTA Angelus and WOLCA cement in the amount of microleakage (P<0.001, Post-hoc Tukey). However; There was a statistically significant difference between MTA Angelus and CAAC cement (p<0.001, Post-hoc Tukey). Conclusion: Given the similarity between the microleakage of WOLCA cement and MTA Angelus, WOLCA is recommended for further clinical and experimental evaluations.