Considering to the possibility of cellular and genetic damage by the implant materials in the patient and the clinician, the safety of the biomaterials should be evaluated. The purpose of this study was to compare the cytotoxicity and genotoxicity induced by two nanocomposites, hydroxyapatite/bioactive glass (HA/BG) and fluorapatite/bioactive glass (FA/BG) in vitro. Biomaterial extracts (BMEX, 100%) were prepared by incubating 100 mg/mL of each biomaterial powder in complete culture medium (RPMI1640 + 10% FBS) for 72 h. Saos-II cells were exposed to different concentrations of BMEXs for different periods of time and evaluated at the end of each period. According to 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay results, both BMEXs at low concentrations (<25%) has no inhibitory effects on the cells growth. After 24 h of exposure, only HA/BG BMEX at 100% concentration showed significant cytotoxic effect. After 48 and 72 h, both HA/BG and FA/BG BMEXs showed similar cytotoxic effect at concentration higher than 75 and 50%, respectively. The results of the comet assay showed that the tail elongation, and proportionally DNA damage, increased in a dose/time dependently fashion with BMEXs exposure. Based on low and similar cytotoxicity and genotoxicity profiles on the Saos-II cell line, it could be concluded that FA/BG, like HA/BG, could be a good candidate for further in vivo biocompatibility studies to be used in bone tissue repair. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 2605-2612, 2018.