Oxidized single-walled carbon nanotubes (o-SWNTs) was modified by covalently and noncovalently linking PEG to the o-SWNTs. The influence of oxidation time, PEG molecular weight, and type of PEG linkage on the blood clearance time of PEG-modified single-walled carbon nanotubes (SWNTs) was investigated. The toxicity profile of SWNTs covalently linked to PEG (c-PEG-o-SWNTs) in rats has also been determined. The pharmacokinetics of c-PEG-o-SWNTs in rats and their distribution in vital organs were monitored by Raman spectroscopy, and the blood clearance of homogenate isoliquiritigenin (ISL) was determined by HPLC. Photos of tissue and tissue sections were taken to evaluate the toxicity of c-PEG-o-SWNTs. We found that SWNTs which were covalently modified with PEG and have a molecular weight of 3500 had the longest blood clearance half-lives. However, SWNTs were toxic to the kidneys and the hearts. The high renal clearance of long-term fate SWNTs may occur because of impaired kidney filtration function. Therefore, we assume that while researchers study the long-term fate of SWNTs, the toxicity of SWNTs also needs to be taken into account.