Background: Attempts for preserving endodontically treated teeth after root canal treatment failure have directed the clinicians to surgical intervention; apicectomies with root end resection followed by placement of root-end filling material. Different techniques are used to assess the quality of the apical seal obtained by root end filling materials. Dye penetration is considered the most popular technique. Objective: this in vitro study aimed to evaluate and compare the apical microleakage of three rootend filling materials.Methods: Twenty one upper incisors were utilized, root canals instrumentation was achieved by ProTaper system. Obturation was conducted by lateral condensation technique using Protaper universal gutta percha points. Teeth were apically resected at an angle of 90° to the long axis of the root and root end cavities were prepared and filled. The samples were coated with varnish, then were immersed in 2% methylene blue solution for 24 hours. Roots were then sectioned bucco-lingually in a longitudinal direction. Extent of dye penetration was detected by the use of stereomicroscope.Results: The highest mean value was recorded in MTA group, followed by Guttaflow bioactive and Endoseal groups, where both almost recorded the same mean values. Tukey's post hoc test revealed no statistically significant difference between the three tested groups. Conclusion:It can be concluded that; all the three groups showed microleakage and none of the three root-end filling materials was able to achieve perfect apical seal. The result also showed that guttaflow bioactive provides a similar reliable seal compared to MTA Fillapex and Endoseal MTA.