The interactions of various polypeptides with individual carbon nanotubes (CNTs), both multiwall (MW) and single wall (SW), were investigated by atomic force microscopy (AFM). While adhesion forces arising from electrostatic attraction interactions between the protonated amine groups of polylysine and carboxylic groups on the acid-oxidized multi-wall carbon nanotubes (Ox-MWCNTs) dominate the interaction at a low pH, weaker adhesion forces via the hydrogen bonding between the neutral -NH2 groups of polylysine and -COO- groups of the Ox-MWCNTs were detected at a high pH. The adhesion force was further found to increase with the oxidation time for Ox-MWCNTs and to be negligible for oxidized single-wall carbon nanotubes (Ox-SWCNTs) because carboxylate groups were only attached onto the nanotube tips in the latter whereas onto both the nanotube tips and sidewall in the former. Furthermore, it was demonstrated that proteins containing aromatic moieties, such as polytryptophan, showed a stronger adhesion force with Ox-MWCNTs than that of polylysine because of the additional pi-pi stacking interaction between the polytryptophan chains and CNTs.