A novel procedure for effective synthesis of covalently oxygen-doped single-walled carbon nanotubes (SWCNTs) has been developed. The SWCNT thin film is directly irradiated by UV light and oxygen atoms substitute into the tube wall via the produced ozone molecules. The photoluminescence spectroscopy studies reveal that the obtained SWCNTs exhibit the characteristic spectroscopic features of epoxide-type oxygen-doped SWCNTs. Advantageously, the emission peak of the doped (6, 5) SWCNTs is centered at around 1300 nm, which is most transparent region of biomaterials. We demonstrate immunoassay, fluorescence vascular angiography and observation of the intestinal contractile activity of mice by using the produced oxygen-doped SWCNTs as infrared fluorescent labels and imaging agents.