Quantification of lipophilic toxins in bivalves associated with diarrhetic shellfish poisoning was investigated by liquid chromatography-mass spectrometry (LC-MS). Using a C8-silica reversed phase column and a mobile phase of aqueous acetonitrile containing 2 mM ammonium formate and 50 mM formic acid, okadaic acid, dinophysistoxin-1, 7-O-palmitoyldinophysistoxin-1, pectenotoxin-1, pectenotoxin-2, pectenotoxin-6, pectenotoxin-2 seco-acid, yessotoxin, and 45-hydroxyyessotoxin in bivalves were quantified by LC-MS in the negative mode. When the crude 90% methanol extracts were analyzed by LC-MS, there were no significant effects from bivalve matrices on the quantification of toxins. More than 200 bivalve samples collected from various production areas in Japan were analyzed by LC-MS. Pectenotoxin-6 and dinophysistoxin-1 were the dominant toxins in scallops and mussels, respectively. Yessotoxin and 45-hydroxyyessotoxin were also detected in both species. Comparison of the quantitative results obtained for these bivalve samples between LC-MS and mouse bioassay indicates that LC-MS is suitable for routine monitoring of lipophilic toxins in Japanese bivalves.