Objectives: Recurrent caries was partly ascribed to lack of antibacterial properties in composite resin. Silver and zinc nanoparticles are considered to be broad-spectrum antibacterial agents. The aim of the present study was to evaluate the antibacterial properties of composite resins containing 1% silver and zinc-oxide nanoparticles on Streptococcus mutans and Lactobacillus. Materials and Methods: Ninety discoid tablets containing 0%, 1% nano-silver and 1% nano zinc-oxide particles were prepared from flowable composite resin (n = 30). The antibacterial properties of composite resin discs were evaluated by direct contact test. Diluted solutions of Streptococcus mutans (PTCC 1683) and Lactobacillus (PTCC 1643) were prepared. 0.01 mL of each bacterial species was separately placed on the discs. The discs were transferred to liquid culture media and were incubated at $37^{circ}C$ for 8 hr. 0.01 mL of each solution was cultured on blood agar and the colonies were counted. Data was analyzed with Kruskall-Wallis and Mann-Whitney U tests. Results: Composites containing nano zinc-oxide particles or silver nanoparticles exhibited higher antibacterial activity against Streptococcus mutans and Lactobacillus compared to the control group (p < 0.05). The effect of zinc-oxide on Streptococcus mutans was significantly higher than that of silver (p < 0.05). There were no significant differences in the antibacterial activity against Lactobacillus between composites containing silver nanoparticles and those containing zinc-oxide nanoparticles. Conclusions: Composite resins containing silver or zinc-oxide nanoparticles exhibited antibacterial activity against Streptococcus mutans and Lactobacillus.