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Increasing reports of blooms of the blue–green alga Cylindrospermopsis raciborskii (C. raciborskii), which contains the hepatotoxic alkaloid cylindrospermopsin (CYN), have led to public health concerns in Australia. The toxicology of CYN appears complex and is still being elucidated. We have utilized the combination of sensitivity and specificity afforded by coupling high performance liquid chromatography (HPLC) to a tandem mass spectrometer (MS/MS) to produce an assay which is suitable for monitoring low CYN concentrations in water samples. Intact algal cells in the water sample are lysed by a freeze–thaw cycle. After filtration (0.45 μm filter), 110 μL is injected. The HPLC uses an Altima C18 (250×4.6 mm, 5 μm) column at 40°C. Chromatography utilizes a linear gradient from 1 to 60% methanol over 5 min, with a final isocratic stage holding at 60% methanol for 1 min. The mobile phase is buffered to 5 mM with ammonium acetate. The transition from the M+H ion (416 m/z) to the 194 m/z fragment is monitored. Linearity of this assay is 1–600 μg/L [peak area=304×CYN (μg/L)−569; r²=1.000 (n=7)]. Using a single point standard curve, total coefficients of variation were 26.4, 10.5, 12.6, and 10.7% at 0.78, 5.2, 104, and 1040 μg/L. This assay is utilized in conjunction with algal cell counts and mouse bioassays to monitor water bodies for public health purposes. The rationale used in employing these methods is discussed. ©1999 John Wiley & Sons, Inc. Environ Toxicol 14: 151–154, 1999