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Fullerene compounds have avid reactivity with free radicals and are regarded as ‘radical sponges’. The trimalonic acid derivative of fullerene is one of the water-soluble compounds that has been synthesized and found to be an effective antioxidant both in vivo and in vitro. Carboxyfullerene has been shown to be effective in the treatment of both Gram-positive and -negative infections, although its mode of action is poorly understood. We determined the MIC and minimal bactericidal concentration of carboxyfullerene for 20 isolates, including Staphylococcus spp., Streptococcus spp., Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa, Salmonella typhi and Klebsiella pneumoniae. We further investigated the action of carboxyfullerene using transmission electron microscopy (TEM), anticarboxyfullerene antibody binding assay and a membrane perturbation assay. All Grampositive species were inhibited by 50 mg/L of carboxyfullerene, whereas Gram-negative species were not inhibited, even at 500 mg/L carboxyfullerene. Bactericidal activity was demonstrated only for Gram-positive species, particularly for Streptococcus pyogenes A-20, which was killed rapidly. Intercalation of carboxyfullerene into the cell wall of staphylococci and streptococci was demonstrated by TEM and anti-carboxyfullerene binding assay. Damage to the cell membrane in Gram-positive, but not Gram-negative, bacteria was confirmed by the membrane perturbation assay. These findings indicate that the action of carboxyfullerene on Gram-positive bacteria is achieved by insertion into the cell wall and destruction of membrane integrity.