Abstract Ca3SiO5 is new cement based on the composition of Portland that has been developed to have superior physicochemical and biological properties. In a clinical evaluation, the cement did not appear to have cytotoxic properties and allowed for the proliferation of pulp cells and gingival fibroblasts. However, no previous studies have evaluated the genotoxicity or the mutagenicity of Ca3SiO5in vivo. Therefore, the goal of this study is to evaluate the genotoxic and mutagenic potential of Ca3SiO5-based cement in vivo. Twenty-four male Wistar rats were divided into 3 groups (n = 8). Group A rats received subcutaneous implantation of Ca3SiO5 in the dorsum. Group B rats received a single dose of cyclophosphamide (positive control). Group C rats received subcutaneous implantation of empty tubes in the dorsum (negative control). After 24 hours, all animals were euthanized and the bone marrow of the femurs was collected for use in the comet assay and the micronucleus test. The comet assay revealed that the Ca3SiO5 group had a tail intensity of 23.57 ± 7.70%, the cyclophosphamide group had a tail intensity of 27.43 ± 7.40%, and the negative control group had a tail intensity of 24.75 ± 5.55%. The average number of micronuclei was 6.25 (standard deviation, SD = 3.53) in the Ca3SiO5 group, 9.75 (SD = 2.49) in the cyclophosphamide group, and 0.75 (SD = 1.03) in the negative control group. There was an increase in the micronuclei frequency in the Ca3SiO5 group compared to that of the negative control group (p < 0.05). Our data showed that exposure to the Ca3SiO5-based cement resulted in an increase in the frequency of micronuclei, but no genotoxicity was detected according to the comet assay.