Silica is among the most popular nanoparticles. Large-scale production and use have increased the risk of human exposure to silica nanoparticles (SiO2NPs). This study aimed to investigate the toxic effects on the kidney, liver and brain of the SiO2NPs. Twenty eight male Wistar albino rats were divided into four groups (n=7 rats) as control (1 mL/day physiological saline administration for 28 day), 6 nm SiO2NP (6 nm, 150 μg/mL/day for 28 day), 20 nm SiO2NP (20 nm, 150 μg/mL/day for 28 day) and 50 nm SiO2NP (50 nm, 150 μg/mL/day for 28 day) groups. After the last administration, rats were sacrificed and kidney, liver and brain samples were taken for biochemical and histological investigation. In all groups, malondialdehyde (MDA) levels, superoxide dismutase (SOD) and catalase (CAT) activities were measured using the spectrophotometric methods. Ultrastructural changes of tissues were evaluated using transmission electron microscopy. In the kidney tissue, the MDA level significantly increased in the 6 and 50 nm groups, while the similar increase was observed in the 6 nm group of the liver and 20 and 50 nm groups of the brain. SOD activity significantly increased in the 6, 20 and 50 nm groups in brain and kidney tissues, but no significant change was observed in the liver tissue groups. Catalase activity decreased in the kidneys at 6 and 50 nm groups and increased in the 20 and 50 nm groups in liver and brain tissues. Ultrastructurally, kidney and liver tissues had normal morphological features in all groups. Degenerative changes were observed in the nerve fibers and axoplasm of myelinated and unmyelinated nerve fibers in 6 nM, 20 nM and 50 nM SiO2NP groups in the brain. These findings showed that exposure to 6, 20 and 50 nm sizes SiO2 NPs may cause toxic effects in the liver, kidney and brain.