Introduction: Effect of biomaterials on proliferation and differentiation of dental pulp stem cells plays a critical role in managing the regeneration of dental tissue. Aim: This research aimed to evaluate and compare the effect of MTA and Biodentine on proliferation and differentiation of dental pulp stem cells. Methods: Dental stem cells were isolated from third molars, and characterized by the proliferation potential of the cells, colongenic capability, multilineage differentiation and the expression of stem cell gene markers. Cell proliferation and viability after application of the experimental materials were evaluated using haemocytometer. The cells odontogenic differentiation potential was evaluated by alizarin red stain and changes in mRNA expressions of odontogenic genes. Results: The two experimental groups initially showed a marked decrease in the proliferation and viability, and then increased without significant difference between the two experimental groups. There was higher statistically significant difference in odontogenic genes expression than control group and the expression of the odontogenic differentiation genes in the biodentine group was statistically significantly higher than that of MTA group. Conclusion: MTA and Biodentine showed favorable cell proliferation, and both were promoted the odontogenic differentiation, and expressed odontoblastic marker genes.