Phytochemical compounds, such as naringin and berberine, have been used for many years due to their antioxidant activities, and consequently, beneficial health effects. In this study, it was aimed to evaluate the antioxidant properties of naringin, berberine and poly(methylmethacrylate) (PMMA) nanoparticles (NPs) encapsulated with naringin or berberine and their possible cytotoxic, genotoxic, and apoptotic effects on mouse fibroblast (NIH/3 T3) and colon cancer (Caco-2) cells. According to the results of the study, it was found that the 2,2-diphenyl-1-picrylhydrazyl (DPPH) inhibition antioxidant activity of naringin, berberine, and naringin or berberine encapsulated PMMA NPs, was significantly increased at higher tested concentrations due to the antioxidant effects of naringin, berberine and naringin or berberine encapsulated PMMA NPs. As a result of the cytotoxicity assay, after 24-, 48- and 72-h of exposure, all of the studied compounds caused cytotoxic effects in both cell lines. Genotoxic effects of studied compounds were not registered at lower tested concentrations. Based on these data, polymeric nanoparticles encapsulated with naringin or berberine may contribute to new treatment approaches for cancer, but further in vivo and in vitro research is required.