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Understanding the factors that contribute to the risk from fish consumption is a relevant public health concern due to potential adverse effects of cyanobacterial toxins. The aim of this work was to study the influence of two usual cooking practices, microwave oven and boiling, on the microcystin (MCs) concentration in fish muscle (Tilapia, Oreochromis niloticus) spiked with a stock solution (500 mu L) containing a mixture of three toxins (MC-LR, MC-RR, and MC-YR) (1.5 mu g/mL of each toxin). Two different variables were investigated: time of cooking in the microwaves treatment (1 or 5 min), and way of boiling, "boiled muscle" or "continuously heated muscle". All samples were then lyophilized and MCs were extracted and purified (Oasis HLB cartridge) and quantified by HPLC-MS. Furthermore, the waters in which the samples boiled were also analyzed after their purification. The results suggest a reduction on MC-LR (36%) and MC-YR (24.6%) in samples cooked in the microwave for 5 min. Major changes were found when the fish was cooked by the continuous boiling, with a decrease of 45.0% (MC-RR), 56.4% (MC-YR) and 59.3% (MC-LR). More studies are necessary to elucidate the mechanisms involved when aquatic food is submitted to usual cooking practices. (C) 2011 Elsevier Ltd. All rights reserved.