AbstractAn electrokinetic immunoassay performed in a chip‐based capillary electrophoresis system is described for the rapid measurement of naproxen in human plasma. The system employs a fluorescently labeled antibody to capture and detect the analyte of interest within a 5 min total assay time with an LOD of 0.025 µg/mL and a saturation level of 450 µg/mL. The system compared well with a conventional HPLC technique but was found to be much faster. Application of the electrokinetic assay to the study of patients with allergy to naproxen demonstrated increased concentrations of the drug extending past the predicted elimination half‐life. The portability of the system and its ability to process up to 18 samples per hour makes it suitable for use in emergency room situations. Copyright © 2006 John Wiley & Sons, Ltd.