In this paper, we reinforced the antifungal activity of multi-walled carbon nanotubes (MWCNTs) using an effective technique. Covalent functionalization of MWCNTs was performed by lysine and arginine under microwave radiation. To prove functionalization phenomenon, the grafted chemical groups on the surfaces of MWCNTs were analyzed by Fourier transform infrared and Raman spectroscopy. Antifungal activities of functionalized MWCNTs as well as pristine MWCNTs were tested against different fungal species based on minimal inhibitory concentration (MIC) and radial diffusion assay. MIC results showed that the antifungal activity of MWCNTs-lysine, in comparison to pristine MWCNTs against fungi, including Aspergillus niger, Aspergillus fumigatus, Candidate albicans, Penicillium chrysogenum, Saccharomyces cerevisiae, Fusarium culmorum, Microsporum canis, Trichophyton mentagrophytes, Trichophyton rubrum and Penicillium lilacinum were increased 1.92, 2.36, 2.35, 1.3, 1.5, 1.1, 2.54, 1.23, 1.42 and 2.1 times, respectively. Similarly, the antifungal activity of MWCNTs-arginine was increased 1.98, 2.40, 2.55, 1.8, 1.9, 1.7, 2.64, 1.36, 2.1 and 2.55 times, respectively. On the basis of the results of this study, it is clearly indicated that covalent groups of lysine and arginine could improve the antifungal activity of MWCNTs. Copyright © 2012 John Wiley & Sons, Ltd.