Silver nanoparticles (SNPs) are widely used in the field of biomedicine, but a comprehensive understanding of how SNPs distribute in the body and the induced toxicity remains largely unknown. The present study was designed to investigate the distribution and accumulation of SNPs in rats with subcutaneous injection. Rats were injected with either SNPs or silver microparticles (SMPs) at 62.8 mg/kg, and then sacrificed at predetermined time points. The main organs of the experimental animals were harvested for ultrastructural analysis by transmission electron microscopy (TEM) and for silver content analysis by inductively coupled plasma mass spectrometry (ICP-MS). Results indicated that SNPs translocated to the blood circulation and distributed throughout the main organs, especially in the kidney, liver, spleen, brain and lung in the form of particles. SMPs, however, could not invade the blood stream, or organ tissues. Ultrastructural observations indicate that those SNPs that had accumulated in organs could enter different kinds of cells, such as renal tubular epithelial cells and hepatic cells. Moreover, SNPs also induced blood-brain barrier (BBB) destruction and astrocyte swelling, and caused neuronal degeneration. The results suggest more cautions needed in biomedical applications of SNPs, in particular, the long-term uses.