Statement of Problem: One of the most challenging procedural accidents during pulpotomy of primary molars is furcal perforation. To prevent bacterial invasion, the perforation site should be sealed as soon as possible.Purpose: The aim of the current study is to investigate the ability of the pro-root MTA and new endodontic cement (NEC) in repairing the furcation perforations of primary molar teeth.Materials and Method: In this in vitro study, 42 extracted primary molars were selected. Their roots were sectioned horizontally and standard access cavity was prepared. The orifices and the root apices were sealed with two layers of resin composite.The samples were randomly assigned into 2 groups. 6 teeth were considered as the positive and the negative controls. In the experimental groups; perforation was made. In group 1 and 2, perforation site received pro-root MTA and NEC respectively. The teeth were covered by two layers of nail polish except for the external surface of the perforation site. The negative control group received no repairing material. All teeth were mounted and sterilized for 24 hours. Lower chambers were filled with sterilized Muller Hinton broth. Bacterial suspension of Enterococcus faecalis in 0.5 McFarland was prepared. The repaired site was then exposed to the bacterial suspension of Enterococcus faecalis every 3 days. All samples were inserted in an incubator at 37oC and 100% humidity. The turbidity of the samples was detected for a period of 30 days. Data were analyzed by Chi- square test.Results: 44% of samples in Pro- root group, 50% of the samples in the NEC group showed contaminations during 30 days. There was no significant difference between these two groups (p= 0.799).Conclusion: With limitations of this study, Pro- root MTA and NEC showed similar capability in sealing the furcal perforations of the primary molars.