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To investigate the effects of 3-aminopropyltriethoxysilane (APTES)- or (3-mercaptopropyl)trimethoxysilane (MPTS)-conditioned nanozirconia fillers on the mechanical properties of Bis-GMA-based resin composites. The conditioned fillers were characterized by Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), and thermodynamic calculations. They were then used to prepare Bis-GMA-based resin composites, whose flexural strength and elastic modulus were evaluated. The Cell Counting Kit-8 (CCK-8) assessed the composites’ cytotoxicity. The FTIR spectra of the conditioned fillers showed new absorption bands at 1569 and 1100 cm –1 , indicating successful grafting of APTES or MPTS onto nanozirconia. XPS confirmed the Zr–O–Si bonds in the APTES- or MPTS-conditioned fillers at contents of 2.02 and 6.98%, respectively. Thermodynamic calculations reaffirmed the chemical binding between the two silanes and nanozirconia fillers. Composites containing the conditioned nanozirconia fillers had significantly greater flexural strengths (APTES, 121.02 ± 8.31 MPa; MPTS, 132.80 ± 15.80 MPa; control, 94.84 ± 9.28 MPa) and elastic moduli (8.76 ± 0.52, 9.24 ± 0.60, and 7.44 ± 0.83 GPa, respectively) than a control with untreated fillers. The cytotoxicity assay identified no significant cytotoxicity by composites containing the conditioned fillers. Silanes were previously considered to be unable to chemically condition zirconia to bond with resin. Inclusion of APTES- or MPTS-conditioned nanozirconia fillers can improve the mechanical properties of Bis-GMA-based resin composites without obvious cytotoxicity in this study.