Multi-walled carbon nanotubes (MWNTs) were assembled on a silica surface using a polyelectrolyte-assisted layer-by-layer (LBL) assembly technique. The surface-assembled silica spheres with MWNTs (MWNTs/SiO(2)), which serve as a novel solid-phase extraction sorbent for separation/pre-concentration of basic proteins, was investigated. The adsorption behavior of cytochrome c (cyto-c) by MWNTs/SiO(2) spheres agrees well with the Langmuir adsorption model. A thorough scrutiny of the experimental parameters affecting the adsorption of cyto-c from aqueous solution onto the MWNTs/SiO(2) spheres and its subsequent desorption was carried out. A maximum adsorption capacity of cyto-c was derived as 112 mg (cyto-c) g(-1) (MWNTs). A distinct feature of the MWNTs/SiO(2)-packed micro-column provides clear advantages of minimized flow impedance when operated in a flow system, in addition to better separation efficiency as well as the favorable enrichment capability of proteins, characterized by an enrichment factor of 30 by using 2.0 mL of aqueous solution. The practical applicability of the MWNTs/SiO(2) spheres as a sorbent for the isolation of basic proteins from acidic protein species was demonstrated by effective separation of cyto-c from bovine serum albumin (BSA).