Root perforations may cause periodontitis, resulting in alveolar bone loss. This study compared the zirconia containing MTA Matreva® (MAT group) to traditional MTA Angelus® (ANG group) as root perforation repair materials regarding the cytotoxicity and the osteogenic potential. Bone marrow mesenchymal stem cells (BM-MSCs) were isolated from two albino rats and cultured. Cytotoxicity of the tested materials was assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay at three-time intervals; 3, 7 and 14 days. The tested materials were used to direct the osteogenic differentiation of BM-MSCs into osteoblasts. Evaluation of osteogenic effect was performed through assessments of calcium deposition by Alizarin red staining (ARS), expression of receptor activator of nuclear factor-kappa B (NF-κB) ligand (RANKL) protein in BM-MSCs seeded on the tested materials for 14 days and osteogenic potential gene markers expression in BM-MSCs after culture on the tested materials for 14 days. The assessed genes included; tumor necrosis factor alpha (TNF-α), transforming growth factor beta (TGF-β), and interleukin 1-β (IL-1β). All data were statistically analyzed. There were no significant differences between ANG and MAT groups in terms of cytotoxicity and osteogenic potential (P>0.05). The highest level of cell proliferation occurred in MAT groups, followed by ANG group, compared to negative controls (NC). The MAT group showed the highest levels of Average % calcific area fraction (90%) followed by that of ANG group (68%) as compared to NC (48%). The BM-MSCs in the MAT group exhibited significantly highest level of RANKL protein expression, followed by that of ANG group. The ANG group revealed significantly greater TNF-α and IL-1β levels than those in NC. The MAT group had significantly greater value of TGF-β than that of NC. Zirconia containing MTA (MTA Matreva) has comparable cytotoxicity and osteogenic potential to traditional MTA (MTA Angelus), which is regarded a dependable material for root perforation healing.