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Silica nanoparticles are widely used for biomedical purposes, but also in cosmetic products, food, the car industry, paints, etc. Considering their mega production, one should not ignore their potential hazardous effects on humans, flora and fauna. Human exposure to nanosilica can occur unintentionally in daily life and in industrial settings. Here, we review the common methods of silica nanoparticle production and its applications in biomedical investigations and nanotoxicology. The use of silica nanoparticles in biomedicine is discussed in terms of drug delivery, their responsiveness to different stimuli, theranostic applications and their uses in the food and cosmetic industries. Advantages and limitations of silica nanoparticles are presented and the effects of these nanoparticles are discussed in relation to their route of entry and impact on biochemical and epigenetic processes in human and animal cells.