The biomedical application of single-walled carbon nanotubes (SWCNTs), such as drug delivery and cancer treatment, requires a clear understanding of their fate and toxicological profile after intravenous administration. In this study, the long-term accumulation and toxicity of intravenously injected SWCNTs in the main organs (such as liver, lung and spleen) in mice were carefully studied. Although SWCNTs stayed in mice over 3 months, they showed low toxicity to mice. The long-term accumulation of SWCNTs in the main organs was evidenced by using Raman spectroscopy and TEM technique. Statistically significant changes in organ indices and serum biochemical parameters (LDH, ALT and AST) were observed. The histological observations demonstrate that slight inflammation and inflammatory cell infiltration occurred in lung, but the serum immunological indicators (CH 50 level and TNF-alpha level) remained unchanged. No apoptosis was induced in the main organs. The decreasing glutathione (GSH) level and increasing malondialdehyde (MDA) level suggest that the toxicity of SWCNTs might be due to the oxidative stress.