Domoic acid, a neurotoxic amino acid produced by the marine diatom Nitchia pungens multiseries, was determined in samples of anchovies, razor clams, mussels, crab, rat serum, urine and feces by HPLC with UV absorption and electrospray (ESI) mass spectrometric (MS) detection. Shellfish samples were extracted with methanol-water followed by clean-up of the extracts with solid-phase extraction cartridges (strong anion or strong cation exchange). An aliquot of the fraction containing the domoic acid was analysed by HPLC. HPLC column size, mobile phase composition and flow-rate were selected so that essentially the same conditions could be used for both HPLC-UV and HPLC-ESI-MS with selected ion monitoring (SIM) determinations. These included the use of acetonitrile-water-formic acid as the mobile phase, at a flow-rate of 0.2 ml/min (split 13:1 for HPLC-ESI-MS-SIM, 10 microliters/min to the mass spectrometer). The results indicated that extracts found positive by the HPLC-UV method could be readily confirmed directly by HPLC-ESI-MS-SIM without additional sample treatment down to levels of 0.1 micrograms/g of domoic acid. This study demonstrates the use of HPLC-ESI-MS-SIM for the routine confirmation of domoic acid in a wide variety of samples.