Organofullerene derivatives have shown a great potential in a wide variety of biological activities such as DNA photocleavage, HIV-protease inhibition, neuroprotection and apoptosis. Among the plethora of functionalized organofullerenes that have been synthesized, fullerene-based amino acids are particularly appealing for structural studies and biological applications. When the fullerene-framework is incorporated into peptides, its original properties can be substantially modified. In addition, the water-solubility of the fullerene derivatives is enhanced, which makes such molecules amenable to biological studies. In this review, recent advances in the growing field of medicinal chemistry of fullerene derivatives will be discussed. Emphasis will be given to the synthesis of the biggest unnatural amino acid 3,4-fulleroproline (Fpr) and its derivatives. For example, Fpr derivatives have been found to interact with different hydrolytic enzymes and selectively discriminate between rationally designed peptides. Fullerene-based peptides have been found to substantially activate enzymes involved in the oxidative deamination of biogenic amines. In addition, their membranotropic properties and effects on the structure and permeability of the lipid bilayer of phosphatidylcholine liposomes as well as the transmembrane transport of bivalent metal ions have been studied. Finally, applications in medicinal chemistry of such types of amino acids and peptides will be highlighted.