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Carbon nanotubes were successfully functionalized for the first time in a free radical phosphonylation reaction. Three synthetic protocols were proposed. Carbon nanotubes and diethylphosphite reacted in the presence of known radical initiator, such as azobisisobutyronitrile, single electron oxidant—Mn(OAc)₃, or under UV radiation. The functionalized material was fully characterized by means of spectroscopic methods, together with microscopic, surface area and thermogravimetric analyses. UV-illumination was found to be the most effective approach for introducing phosphonates onto carbon nanotubes. X-ray photoelectron spectroscopy analysis showed 6% phosphorus in this sample. Moreover, the method was performed at room temperature for only one hour, using diethylphosphite as a reactant and as a solvent. The functionalized carbon nanotubes showed an improved thermal stability, with a decomposition onset temperature increase of more than 130 °C. This makes it very promising material for flame retarding applications.