Silicon is one of the most abundant chemical elements found on the Earth. Due to its unique chemical and physical properties, silicon based materials and their oxides (e.g. silica) have been used in several industries such as building and construction, electronics, food industry, consumer products and biomedical engineering/medicine. This review summarizes studies on effects of silicon and silica nano- and micro-particles on cells and organs following four main exposure routes, namely, intravenous, pulmonary, dermal and oral. Further, possible genotoxic effects of silica based nanoparticles are discussed. The review concludes with an outlook on improving and standardizing biocompatibility assessment for nano- and micro-particles.