The purposes of this study were to compare the efficacy of irrigation systems by removing a calcium hydroxide (Ca(OH)2) paste from the apical third of the root canal and the effect of the patency file. Sixty single rooted human teeth were used in this study. The canals were instrumented by a crown-down manner with .04 taper ProFile to ISO #35. Ca(OH)2 and distilled water were mixed and placed inside the root canals. The teeth were divided into 6 groups according to the root canal irrigation system and the use of patency file as follows: group 1 - conventional method; group 2 - EndoActivator(R); group 3 - EndoVac(R); group 4 - conventional method, patency; group 4 - EndoActivator(R), patency; group 6 - EndoVac(R), patency. All teeth were irrigated with sodium hypochlorite. After the root canal irrigation, the teeth were split in bucco-lingual aspect. Percentage of the root canal surface coverage with residual Ca(OH)2 until 3 mm from working length was analyzed using Image Pro Plus ver. 4.0. Statistical analysis was performed using the One-way ANOVA, t-test and Scheffe's post-hoc test. Conventional groups had significantly more Ca(OH)2 debris than EndoActivator(R), EndoVac(R) groups. There was no significant difference between EndoActivator(R) and EndoVac(R) groups. Groups with patency file showed more effective in removing Ca(OH)2 paste than no patency groups, but, it was no significant difference. This study showed that EndoActivator(R) and EndoVac(R) systems were more effective in removing Ca(OH)2 paste from the apical third of the root canal than conventional method.