Immediate sealing of furcation perforations enhances the repair process. The purpose of this study was to longitudinally compare the ability of mineral trioxide aggregate (MTA) and Super-EBA to seal furcation perforations. Fifty-one extracted human maxillary molars were decoronated 3 mm above the CEJ, and the roots were amputated 3 mm below the furcation. A #2 high-speed round bur was used to perforate the center of the furcations. The canals were obturated with gutta-percha, and the root ends were sealed with C&B Metabond. Three experimental groups of 15 teeth each were restored with MTA, Super-EBA, or a combination of MTA in the perforation and a Super-EBA dome on the pulpal floor. Six teeth served as controls. Each tooth was affixed to a fluid filtration device and subjected to a pressure of 20 cm H2O. The integrity of the perforation seal was evaluated initially at 30 min for the Super-EBA and the combination groups and at 4 h for the MTA group. Additional measurements were then made at 24 h, 1 week, and 1 month. The controls behaved as expected. A two-way ANOVA revealed a significant difference (p = 0.01) between materials. Tukey's test isolated the difference to Super EBA as producing a superior seal but only at 24 h. There was no significant effect with time (p = 0.57) or the interaction of the materials with time (p = 0.66). All materials sealed the perforations very well. The maximum leakage of all materials was <0.007 microL min(-1) cm H2O(-1).