As the biosafety of nanotechnology becomes a growing concern, the in vivo nanotoxicity of NPs has drawn a lot of attention. Silica nanoparticles (SiNPs) have been widely developed for biomedical use, but their biodistribution and toxicology have not been investigated extensively in vivo. Although investigations of in vivo qualitative distribution of SiNPs have been reported, the time-dependent and quantitative informations about the distribution of SiNPs are still lacking. Here we investigated the long-term (30 days) quantitative tissue distribution, and subcellular distribution, as well as potential toxicity of two sizes of intravenously administered SiNPs in mice using radiolabeling, radioactive counting, transmission electron microscopy and histological analysis. The results indicated that SiNPs accumulate mainly in lungs, liver and spleen and are retained for over 30 days in the tissues because of the endocytosis by macrophages, and could potentially cause liver injury when intravenously injected.