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Carbon nanotubes (CNTs) have been widely applied in various fields due to excellent physical and chemical properties. As production and applications of nanotubes expand, public concern about their potential risks to human health has also risen. In the present study, the effects of CNTs on rat liver and brain by single intratracheal instillation were detected. CNTs [either single-walled carbon nanotubes (SWCNTs) or multi-walled carbon nanotubes (MWCNTs)] could be seen in the lung and liver indicating the transfer of CNTs by blood stream. CNTs could induce oxidative stress in liver with elevated Malondialdehyde (MDA) level and degressive GSH level, superoxide dismutase (SOD) and CAT activity. To brain, maybe due to the blood brain barrier and the increased SOD and CAT activity, serious oxidative stress of brain did not occur.