The adsorption of molecules in a confined environment (pores and narrow channels) differs from adsorption on flat surfaces. While the immobilization of proteins on porous carbon and the transport of protein molecules through carbon nanotube channels are of great practical importance, the interaction of proteins with the carbon surface in confinement is poorly understood. In this study the adsorption of bovine serum albumin (BSA) and tumor necrosis factor-α(TNF-α)was studied in carbon nanotubes grown by chemical vapor deposition in cylindrical pores of anodic alumina membranes. BSA adsorption depends on the channel diameter of the carbon nanotubes, the termination of nanotube surfaces (surface chemistry), and the pH of medium. Amination of the carbon surface leads to increased adsorption of the proteins at neutral pH, while oxidation decreases the sorption capacity. The differences have been explained by favorable or unfavorable electrostatic interactions between protein molecules and the carbon surface.