A new phase containing immobilized carbon nanotubes (CNTs) was synthesized by in situ polymerization of acid-treated multi-walled CNTs using butylmethacrylate (BMA) as the monomer and ethylene dimethacrylate as the crosslinker on a silanized capillary, forming a porous-layered open-tubular column for CEC. Incorporation of CNT nano-materials into a polymer matrix could increase the phase ratio and take advantage of the easy preparation of an OT-CEC column. The completed BMA-CNT column was characterized by SEM, ATR-IR, and EOF measurements, varying the pH and the added volume organic modifier. In the multi-walled CNTs structure, carboxylate groups were the major ionizable ligands on the phase surface exerting the EOF having electroosmotic mobility, 4.0 x 10(4) cm(2) V-1 S-1, in the phosphate buffer at pH 2.8 and RSD values (n = 5), 3.2, 4.1, and 4.3%, for three replicate capillaries at pH 7.6. Application of the BMA-CNT column in CEC separations of various samples, including nucleobases, nucleosides, flavonoids, and phenolic acids, proved satisfactory upon optimization of the running buffers. Their optima were found in the borate buffers at pH 9.0/50 mM, pH 9.5/10 mM/50% v/v ACN, and pH 9.5/30 mM/10% v/v methanol, respectively. The separations could also be used to assess the relative contributions of electrophoresis and chromatography to the CEC mechanism by calculating the corresponding velocity and retention factors. Discussions about interactions between the probe solutes and the bonded phase included the pi-pi interactions, electrostatic repulsion, and hydrogen bonding. Furthermore, a reversed-phase mode was discovered to be involved in the chromatographic retention.