Carbon-based nanomaterials (CNMs) have emerged as platforms for biological imaging due to their low toxicity and their ability to be internalized by cells. Members of the CNMs family are fullerenes, carbon nanotubes (CNTs), graphene derivatives, nanodiamonds (NDs), carbon dots (CDs), and carbon nano-horns (CNHs). Their peculiar C–C network and nano-size dimensions confer interesting electronic, optical, thermal, and mechanical properties on them. In this chapter, we will distinguish between CNMs that have intrinsic fluorescence, with high photo-stability and low tendency to photobleach, and those that can become fluorescent after appropriate physical and chemical treatments. We will underline their favorable characteristics, such as biocompatibility, easy synthetic procedures, low production cost, and versatile chemical functionalization, which make them ideal candidates for biotechnological applications.