In this study, we investigated water-dispersible surface modification for size- and shape-controlled fullerene nanoparticles (C60P) based on a condensation reaction with di-amino alkane. This modification provided for water dispersibility of C60P and the capability for secondary modification as well. The resultant C60P particles have several useful physical properties: water-dispersibility for ease of injection; fluorescence for detection and quantification; and a characteristic morphology to assist identification. These properties will widely extend the applications of these particles, especially into the biological fields of bioimaging and drug delivery.