INTRODUCTION: Mineral trioxide aggregate is being widely used for root end filling, pulp capping, perforation repair, and other endodontic procedures. Recently, a material similar to ProRoot mineral trioxide aggregate (PMTA) was developed in Iran named Root mineral trioxide aggregate (RMTA) with the claim of having the exact result of original MTA. The purpose of this study was to compare the amount of cell cytotoxicity of RMTA with PMTA at three different time periods using scanning electron microscopy (SEM) as well as the amount of cell viability at the above mentioned period. MATERIALS AND METHODS: Three culture plates in each group were packed with a homogenous layer of PMTA and RMTA prepared according to manufacturers instruction. A plate of media without any material was used as control in each group. The material set for 72 h in CO2 incubator and 2x10 of fibroblast L929 was added to each plate. SEM evaluation with x800-3000 magnification and cell viability counting using trepan blue counting method were done after 48, 72, and 168 hours. RESULTS: There was no significant difference between cell viability of PMTA and RMTA, although the amount of cells remained viable in PMTA group was higher at 48 and 168 hours while for RMTA, it was higher after 72 hours. The SEM evaluation showed that PMTA compared with RMTA has less porosity, but relatively similar amount of cell coverage was detected for both materials after 168 hours. CONCLUSION: ProRoot and Root MTAs showed comparative biocompatibility while evaluated in vitro. The results suggest that RMTA can be used as an alternative for PMTA in clinical trials.