Considering the popular use of microwave ovens to prepare foods, inhibitory effect of microwave cooking on foodborne pathogens was studied. Whiting and salmon blocks were inoculated either with E. coli O157:H7, Staphylococcus aureus or Listeria monocytogenes, then cooked in microwave oven to the internal temperatures of 50 and 70 degrees C. Cooking of fish fillets to both internal temperatures resulted in approximately 4 log cfu/cm(2) reductions in E. coli O157:H7 population. After cooking to the internal temperatures of 50 degrees C S. aureus counts reduced by 2.78 and 1.06 log cfu/cm(2) on whiting and salmon fillets, respectively. L. monocytogenes counts reduced by 1.70 and 0.14 log cfu/cm(2) on whiting and salmon fillets, respectively, cooked to 50 degrees C. S. aureus and L. monocytogenes counts reduced below detectable level (2 log cfu/cm(2)) when cooked to 70 degrees C. The results suggest that internal temperature should be higher than 70 degrees C during microwave cooking to destroy completely these pathogens. Practical applications This research shows that pathogens of Listeria monocytogenes, Staphylococcus aureus and E. coli O157: H7 cannot be completely inhibited by microwaving at 50 and 70 degrees C (internal temperatures) in both fish species. The findings revealed that using a microwave oven to cook fish could be a problem regarding pathogen inactivation in terms of food safety and human health. The study may also help microwave oven producers and caterers to prepare the manufacturer's recommendations, and to determine CCPs in HACCP plans.