A simple, rapid and sensitive method was developed for the simultaneous quantification of chlorogenic acid (CGA) and caffeic acid (CA) in rat plasma using a high-performance liquid chromatography system coupled to a negative ion electrospray mass spectrometric analysis. The plasma sample preparation was a simple deproteinization by the addition of two volumes of acetonitrile followed by centrifugation. The analytes and internal standard ferulic acid were separated on an Intersil C8-3 column (5 mm; 250 × 2.1 mm) with acetonitrile/0.05% triethylamine solution (70:30, v/v) as mobile phase at a flow rate of 0.2 mL/min with an operating temperature of 30°C. Detection was performed on a quadrupole mass spectrometer equipped with an electrospray ionization (ESI) source operated in selected ion monitoring (SIM) mode. Negative ion ESI was used to form deprotonated molecules at m/z 353 for chlorogenic acid, m/z 179 for caffeic acid, and m/z 193 for the internal standard ferulic acid. Linear detection responses were obtained for CGA concentrations ranging from 0.005 to 2.0 µg/mL and for CA concentrations ranging from 0.010 to 2.0 µg/mL and the lower limits of quantitation (LLOQs) for CGA and CA were 0.005 and 0.01 µg/mL, respectively. The intra- and inter-day precisions (RSD%) were within 9.0% for both analytes. Deviation of the assay accuracies was within ±10.0% for both analytes. Their average recoveries were greater than 88.0%. Both analytes were proved to be stable during all sample storage, preparation and analytic procedures. The method was successfully applied to the pharmacokinetic study of CGA and CA following an intravenous dose of 5 mL/kg mailuoning injection to rats. Copyright © 2006 John Wiley & Sons, Ltd.