Statement of problem: Root perforation is a procedural error that can have a profound effect on treatment prognosis. Treatment prognosis is dependent on the prevention or the treatment of bacterial infection at the perforation site. Therefore, using a biocompatible material to completely seal the perforation is of paramount importance.Purpose: The purpose of this study was to evaluate and compare the ability of Pro Root MTA and Portland cement to seal furcal perforations in the extracted human molar using dye penetration.Materials and Method: In this experimental in vitro study, 70 human permanent mandibular molars with well developed, non-fused, minimum caries and without anomalies were used. Access openings and furcation perforations were prepared in the pulp chamber floor. Ten teeth were assigned as controls and divided into two groups of five teeth each as positive and negative control. The positive group was accessed and perforated similar to the experimental group while the negative controls were not prepared. The remained 60 teeth were divided into two groups of 30 teeth each. Group A1 was repaired with Pro Root MTA and group A2 was repaired with Portland cement. The teeth were submerged in Indian ink for 4 days. Finally, the samples were sectioned and evaluated for linear dye penetration at 6x magnification and then the data were statistically analyzed by Mann-Whitney test.Results: The result showed that the sealability of Pro Root MTA and Portland cement in furcation perforations was not statistically different ( p >0.05).Conclusion: In accordance with high expenses of Pro Root MTA and the same ability of Portland cement and Pro Root MTA in sealing of furcation perforation, the Portland cement could be a good alternative for Pro Root MTA for this purpose.Key words: Furcal perforation, Pro Root MTA, Portland cement