The racemic naproxen was selectively recognized by capillary electrochromatography (CEC) on an (S)-naproxen-imprinted monolith, which was prepared by an in situ thermal-initiated polymerization. The recognition selectivity of a selected monolith strictly relied on the CEC conditions involved. The factors that influence the imprinting selectivity as well as the electroosmotic flow (EOF), including the applied voltage, organic solvent, salt concentration and pH value of the buffer, column temperature, and surfactant modifiers were systematically studied. Once the column was prepared, the experiment results showed that the successful chiral recognition was dependent on CEC variables. For example: the recognition could be observed in acetonitrile and ethanol electrolytes, while methanol and dimethyl sulfoxide (DMSO) electrolytes had no chiral recognition ability. The buffer with pH values of 2.6 or 3.0 at a higher salt concentration had chiral recognition ability. Column temperatures of 25-35degreesC were optimal. Three surfactants, sodium dodecyl sulfate (SDS), cetyltrimethylammoniurn bromide (CTAB), and polyoxyethylene sorbitan monolaurate (Tween 20), can improve the recognition. Baseline resolution was obtained under optimized conditions and the column efficiency of the later eluent (S)-naproxen was 90 000 plates/m.