Background: Silica nanoparticles (SiO2 NPs) are widely used in industrial products as additives for rubber and plastics or as filler strengthening concrete, as well as being used in the biomedical field for drug delivery and theranostic purposes. The present study investigated the effects of amino or carboxyl functionalization of rhodamine-labeled SiO2 NPs on cellular uptake and cytotoxicity. Methods: Male mice were randomly divided into seven groups (n=6, each) and exposed to non-functionalized (plain), carboxyl or amino-functionalized rhodamine-labeled SiO2 NPs at 2 or 10 mg/kg bw, or endotoxin-free water, by pharyngeal aspiration. At 24 hours after administration, the mice were euthanized and bronchoalveolar lavage fluid (BALF) was collected for differential cell count and identification of silica nanoparticle uptake using confocal microscopy. In the in vitro studies, murine RAW264.7 macrophages were exposed to non-functionalized, amino- or carboxyl-functionalized Rhodamine-labeled SiO2 NPs. Nonspecific caspase inhibitor and necrostatin-1 were used to determine the involvement of caspase or receptor-interacting protein 1 kinase domain in the cytotoxicity. Results: The in vivo study demonstrated that the neutrophil and macrophage counts and the percentage of macrophages with internalized particles was highest in the order of carboxyl >= amino- > > non-functionalized particles. The in vitro study demonstrated greater cytotoxicity for non-functionalized silica nanoparticles, compared to the others. Treatment with non-specific caspase or necroptosis inhibitor did not attenuate MTS cytotoxicity of non-functionalized silica nanoparticles. Conclusion: We conclude that carboxyl-functionalzed SiO2 NPs are internalized by macrophages more efficiently but less cytotoxic than plain SiO2 NPs. The cytotoxic effect of plain SiO2 NPs, which cannot be explained by apoptosis or necroptosis, can be avoided by carboxyl- or amino- functionalization.