Microwave cooking has increased in popularity in recent years. Since the time to process food is much shorter than with conventional methods, questions have been raised as to the microbial safety of foods cooked with microwaves. The first part of this review includes discussions on the importance of intrinsic and extrinsic characteristics of foods in relation to destruction of microorganisms in microwave-cooked foods, the mechanism of microwave destruction of microorganisms and viewpoints on the thermal and nonthermal destruction of microorganisms. The second part includes data on the effect of time and temperature on microorganisms in microwave-cooked foods, the effect of microwave destruction of microorganisms in different food systems and the effect of microwaves on different bacteria. The last section includes discussions of destruction of microorganisms by microwave cooking of meats, poultry and egg products, dairy products, cereal products, fruit products, vegetables and miscellaneous foods. We observed that (a) microwave heating of food is more “food dependent” than conventional heating, (b) the manufacturer-recommended microwave treatment time for some foods may not destroy high levels of bacteria, (c) use of microwaves in combination with other conventional heating methods results in more uniform heating in foods and destruction of bacteria, (d) heat generated by microwaves kills naturally-occurring microorganisms as long as the size and type of food are carefully correlated with exposure time, (e) microwaves exert different killing effects on individual bacterial species and (f) the question of thermal versus nonthermal effects of microwaves on microorganisms has not been settled. We believe microwave heating is an important method for processing of foods at home, in institutions and in commercial operations. The process is acceptable from the standpoint of food spoilage and food safety as long as the users understand the limitations and possibilities of microwave heating and are aware of some of the major points presented in this review.