Azaspiracids, a new class of shellfish toxins, have been implicated in several recent incidents of human intoxications following the consumption of mussels (Mytilus edulis). A study was undertaken to examine the distribution of azaspiracid poisoning (AZP) toxins in scallops (Pecten maximus) and individual shellfish were dissected into five tissue fractions for the determination of toxin composition. Separation of the predominant azaspiracids, AZA1-3, was achieved using reversed-phase liquid chromatography with detection by positive electrospray multiple tandem mass spectrometry. The AZP toxin composition was determined in the adductor muscle (meat), gonad (roe), hepatopancreas (digestive glands), mantle and gill of scallops. Substantial differences in the AZP toxin levels between tissue compartments were observed and toxins were concentrated predominantly, about 85%, in the hepatopancreas. There was also a significant variation in the total toxin levels between individual scallops from the same sample batch and the RSD was 60% (n = 9). Interestingly, although all three AZP toxins were present in phytoplankton and mussels, AZA3 was not detected in the scallop samples examined. It was concluded that to improve food safety, only the adductor muscle and gonad of scallops should be permitted for sale to the public.