A capillary electrochromatography (CEC) method has been developed for the separation of caffeine and its two metabolites 1-methylxanthine (1-MX) and 1,7-dimethylxanthine (1,7-DX). The stationary phase was 3-(1,8-naphthalimido) propyl-modified silyl silica gel (NAIP) and the best separations were achieved with 4.0 mm citrate buffer (pH 5.0) containing 80% methanol at an applied voltage of 25 W The compounds were completely separated in less than 3.5 min with good repeatability, which was approximately 3-times less than that in high-performance liquid chromatography (HPLC) with NAIR The proposed method coupled with microdialysis was successfully applied to the monitoring of caffeine concentration in rat brain with detection limits of 1.11 mug/mL.