The interactions of single-walled carbon nanotubes (SWNTs) with ferritin protein in water were investigated. It was found that SWNTs are naturally protein-affinitive in an aqueous ferritin solution, resulting in significant ferritin-SWNT conjugation and the solubilization of the nanotubes. The conjugation is further enhanced and stabilized in the presence of a coupling agent for amidation to promote the formation of covalent linkages. The natural protein-affinity of SWNTs may be alleviated or even eliminated by the functionalization of the nanotubes with hydrophilic polymers or better with oligomeric poly(ethylene glycol) moieties.