A sensitive and specific liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) method has been developed and validated for the identification and quantification of berberine and palmatine in rat plasma. After the addition of the internal standard (IS) and alkalization with 0.5M sodium hydroxide solution, plasma samples were extracted by ethyl ether and separated by HPLC on a Shim-pack ODS (4.6 microm, 150 mm x 2.0mm i.d.) column using a mobile phase composed of A (0.08% formic acid and 2 mmol/l ammonium acetate) and B (acetonitrile) with linear gradient elution. Analysis was performed on a Shimadzu LC/MS-2,010A in selected ion monitoring (SIM) mode with a positive electrospray ionization (ESI) interface. [M](+)=336 for berberine; 352 for palmatine and [M+H](+)=340 for IS were selected as detecting ions, respectively. The method was validated over the concentration range of 0.31-20 ng/ml for berberine and palmatine. Inter- and intra-CV precision (R.S.D.%) were all within 15% and accuracy (%bias) ranged from -5 to 5%. The lower limits of quantification were 0.31 ng/ml for both analytes. The extraction recovery was on average 68.6% for berberine, 64.2% for palmatine. The validated method was used to study the pharmacokinetic profile of berberine and palmatine in rat plasma after oral administration of Huang-Lian-Jie-Du decoction.