Introduction: MTA has been recommended primarily as a root end filling material, but it has also been used in pulp capping, pulpotomy, apical barrier formation in teeth with open apexes, repair of root perforations, and root canal filling. Objectives: This study is designed to evaluate the biocompatibility and bone healing of MM-MTA in comparison to MTA. Materials and Methods: This study was conducted on 30 rats by making osteotomies on both sides of the mandibles of the rats. Fifteen rats were sacrificed after one week to evaluate the short term inflammatory response and bone healing and the other fifteen were sacrificed after three weeks to evaluate the long term inflammatory response and bone healing. Specimens were collected for histopathological examination under light microscope and histomorphometric examination. Results: Grey ProRoot MTA showed significantly lower inflammatory reaction than MM-MTA, and no statistical significant difference was recorded between the two materials in the histomorphometric analysis. Conclusions: MM-MTA and Grey ProRoot MTA showed comparable biocompatibility when evaluated in vivo. Although the results are supportive for the Grey ProRoot MTA showing more biocompatibility compared to MM-MTA, both materials are considered to be equivalent in the ability of the formation of bone.