Anatoxin-a (AN) and homoanatoxin-a (HMAN) are potent neurotoxins produced by a number of cyanobacterial species. A new, sensitive liquid chromatography/multiple tandem mass spectrometry (LC/MSn) method has been developed for the determination of these neurotoxins. The LC system was coupled, via an electrospray ionisation (ESI) source, to an ion-trap mass spectrometer in positive ion mode. The [M+H]+ ions at m/z 166 (anatoxin-a) and m/z 180 (homoanatoxin-a) were used as the precursor ions for multiple MS experiments. MS2MS4 spectra displayed major fragment ions at m/z 149 (AN), 163 (HMAN), assigned to [MNH3+H]+; m/z 131 (AN), 145 (HMAN), assigned to [MNH3H2O+H]+, and m/z 91 [C7H7]+. Although the chromatographic separation of these neurotoxins is problematic, reversed-phase LC, using a C18 Luna column, proved successful. Calibration data for anatoxin-a using spiked water samples (10 mL) in LC/MSn modes were: LC/MS (25–1000 μg/L), r2 = 0.998; LC/MS2 (5–1000(μg/L), r2 = 0.9993; LC/MS3 (2.5–1000 μg/L), r2 = 0.9997. Reproducibility data (% RSD, N = 3) for each LC/MSn mode ranged between 2.0 at 500 μg/L and 7.0 at 10 μg/L. The detection limit (S/N = 3) for AN was better than 0.03 ng (on-column) for LC/MS3 which corresponded to 0.6 μg/L. Copyright © 2003 John Wiley & Sons, Ltd.