Objectives. To evaluate the effect of apical foramen diameter and apical barrier thickness on the sealing ability of mineral trioxide aggregate (MTA) and calcium enriched mixture (CEM) plugs in open apices. Materials and Methods. The fluid filtration method was conducted on a total of 136 roots. Samples were randomly divided into two control (n = 8) and four experimental groups (n = 30). Apical foramen diameters measuring 1.1 and 1.7 mm were shaped for groups "1 and 3" and "2 and 4", respectively. In groups 1 and 2 MTA plug and in groups 3 and 4 CEM plug was inserted. The groups were further divided into subgroups according to the thickness of the apical plugs (3- or 5-mm). Microleakage was measured at 1, 7, and 30 days. Results. Mixed ANOVA test showed that the microleakage in groups 1 and 3 as well as all 5-mm plug subgroups were significantly less than groups 2 and 4 (P < 0.05) and 3-mm subgroups (P < 0.05), respectively. Microleakage was significantly lower at 30th day (P < 0.05). Conclusions. Reducing canal diameter or increasing apical plug thickness and the time interval increases the sealing ability of apical barriers. Furthermore, in comparison to MTA, CEM plugs demonstrated superior sealing ability.