The effect of cooking on the concentration and burden of domoic acid in two bivalve molluscs was studied. The Manila clam (Ruditapes philippinarum) and cockle (Cerastoderma edule) were subjected to steaming and boiling, respectively. In both cases, factorial plans were used to evaluate the effects of common cooking methods and the variations likely to take place during the cooking procedure (cooking time and salt concentration in both species, in addition to ethanol percentage in Manila clam). The domoic acid concentration and toxin content were affected by cooking in very different ways in the two species studied. The cockle lost a significant part of its domoic acid content, while the clam did not. Since the weight of the soft tissues in cooked bivalves was lower than in the raw samples in both species, the toxin concentration decreased less than the toxin burden in the cockle, while it increased in the clam, where the toxin burden did not change significantly. Among the cooking variables tested, only cooking time had a noticeable effect on the domoic acid content in the clam and cockle, with the bivalves that were cooked for a longer time having smaller amounts of toxin. It is clear that cooking affects the toxin concentration in bivalves in a way that is species specific. This characteristic must be taken into account when evaluating epidemiological information, establishing allowable toxin levels and in cases where pre-processing treatments such as cooking or similar methods are used in monitoring systems.