Carbon nanoparticles are in all of the carbon nanomaterials that are presently widely pursued for potential bioapplications, but their in vivo biodistribution-related properties are largely unknown. In this work, highly (13)C-enriched carbon nanoparticles were prepared to allow their quantification in biological samples by using isotope-ratio mass spectroscopy. The in vivo biodistribution results are presented and discussed, and also compared with those of the aqueous suspended carbon nanotubes reported previously. The distribution profile and time dependencies are largely similar between the nanoparticles and nanotubes, with results on both suggesting meaningful accumulation in some major organs over an extended period of time. Therefore, the surface modification of carbon nanoparticles, preferably the chemical functionalization of the nanoparticles with biocompatible molecules or species, is desirable or necessary in the pursuit of these nanomaterials for various bioapplications.