Carbon nano-onions (CNOs) are an emerging class of nanoparticles which shows great potential in a number of different applications. Carbon nano-materials have been widely explored in biological cell imaging, due to their lack of toxicity, and biosafety. Recently, the rapid development and availability of chemical surface modification methods have made it possible to explore these cage-in-cage structured nanoparticles as novel systems for biological applications. The functionalization of CNOs with different functional groups improves their solubility and biocompatibility, resulting in an increased ability to penetrate into the cells. Moreover, their small size and high surface area allow for the conjugation of different diagnostic and therapeutic agents, opening new avenues in theranostic applications. In this review article, we discuss the latest advances reported by our group regarding the use of CNOs for biomedical applications and our findings confirm their great potentiality as promising platform for novel therapeutic approaches.