Over the past decade, carbon nanostructures (CNSs) have been widely used in a variety of biomedical applications. Examples are the use of CNSs for drug and protein delivery or in tools to locally dispense nucleic acids to fight tumor affections. CNSs were successfully utilized in diagnostics and in noninvasive and highly sensitive imaging devices thanks to their optical properties in the near infrared region. However, biomedical applications require a complete biocompatibility to avoid adverse reactions of the immune system and CNSs potentials for biodegradability. Water is one of the main constituents of the living matter. Unfortunately, one of the disadvantages of CNSs is their poor solubility. Surface functionalization of CNSs is commonly utilized as an efficient solution to both tune the surface wettability of CNSs and impart biocompatible properties. Grafting functional groups onto the CNSs surface consists in bonding the desired chemical species on the carbon nanoparticles via wet or dry processes leading to the formation of a stable interaction. This latter may be of different nature as the van Der Waals, the electrostatic or the covalent, the π-π interaction, the hydrogen bond etc. depending on the process and on the functional molecule at play. Grafting is utilized for multiple purposes including bonding mimetic agents such as polyethylene glycol, drug/protein adsorption, attaching nanostructures to increase the CNSs opacity to selected wavelengths or provide magnetic properties. This makes the CNSs a very versatile tool for a broad selection of applications as medicinal biochips, new high-performance platforms for magnetic resonance (MR), photothermal therapy, molecular imaging, tissue engineering, and neuroscience. The scope of this work is to highlight up-to-date using of the functionalized carbon materials such as graphene, carbon fibers, carbon nanotubes, fullerene and nanodiamonds in biomedical applications.