Effect of sidewall carboxylation on protein adsorption behavior of multi-walled carbon nanotubes (MWCNTs) was studied. Two water-soluble proteins, bovine serum albumin (BSA) and egg white lysozyme (LYS), were employed in this work. Carboxylation of MWCNTs suppressed adsorption of BSA, whereas adsorption of LYS was enhanced by the carboxylation. These behaviors are explained by the difference in the dominance of hydrophobic interaction and ionic interaction between MWCNTs and the proteins.