This paper reports a novel approach for developing a microfluidic electrochromatographic chip device using patterned vertically aligned carbon nanotubes as the stationary phase material. Patterned growth of nanotubes in a specific location of the channel is carried out using a solid phase Fe–Al catalyst as well as a vapor deposited ferrocene catalyst. Proof-of-concept applications are demonstrated using reversed phase capillary electrochromatographic separations as well as solid phase extraction of a glycosylated protein using concanavalin A immobilized onto the nanotube bed.