The purpose of the present study was to evaluate and compare between Mineral trioxide aggregate (MTA) and Portland cement (PC) regarding sealing ability in furcation perforation repair and antibacterial activity aganist two strains of bacteria alone or using 10% calcium chloride (CaCl2) and 2% chlorhexidine (CHX) as additives either separately or in combination. The dye extraction method was used to assess sealing ability and the direct contact method was used to assess antibacterial ability. For the sealing ability study, ninety-two extracted, human permanent mandibular first molars were used. The occlusal surface of the crowns were reduced to 3 mm coronal to cemento-enamel junction, and the roots were amputated 3 mm apical to furcation area. Flowable composite was used to seal orifices of the canals. Teeth were covered by 2 layers of nail polish. Perforations were made in furcation area using a size #4 round bur. They received the repair materials, so that eight experimental groups (n=10) were made: MTA, (MTA/CaCl2), (MTA/CHX), (MTA/Comb), PC, (PC/CaCl2), (PC/CHX), (PC/Comb). The remaining twelve samples were equally divided into positive and negative control groups. In the positive control group (n=6), the perforations were left unfilled, while in the negative control group (n=6), the samples had no perforations. Materials were left for 2 days to set. The coronal cavity of each sample was then filled with 2% neutral buffered methylene blue solution for 48 h.