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The AOAC Mouse Bioassay method (MBA) has been widely used for routine monitoring of paralytic shellfish poisoning (PSP) for more than 50 years. However, this method has low sensitivity and experiences interference from other components in the extract. Also, ethical issues have been raised against the continued use of this live-mouse assay. To establish an alternative method for PSP analysis, we attempted to develop PSP analysis conditions using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The LC-MS/MS analysis of reference material showed very reasonable accuracy, and the analysis time was just 15 min. However, the recovery rate of toxin spike samples using the LC-MS/MS analysis was 59.4-91.0%. We also attempted to remove the matrix effect using shellfish extracts, but recoveries of C1 and C2 did not improve. A comparison between the results of MBA and LC-MS/MS analysis revealed good correlations, with values of 0.8878 and 0.9211 for oyster and mussel matrices, respectively.