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Functionalized multi-wall carbon nanotubes (MWCNTs) have been embedded in a rubber-toughened epoxy formulation in order to explore the possibility to impart an auto-repair function to the epoxy matrix. The nanofiller has been covalently functionalized with hydrogen bonding moieties able to act as donor and acceptor of hydrogen bondings. Healing efficiencies have been evaluated for nano charged epoxy formulations at a loading of 0.5% wt/wt of functionalized MWCNTs bearing barbituric acid and thymine-based ligands. For both the performed functionalizations, a self-healing efficiency higher than 50% has been found. Dynamic Mechanical Analysis (DMA) highlights that the inclusion of nanofiller increases the storage moduli. Furthermore, DMA analysis evidences the presence of a phase characterized by a greater mobility of the epoxy chains, which promotes the activation of self-healing mechanisms.