Uneven cooking due to consumer use of microwave ovens to cook food products that have been prepared but are not ready to eat has been a documented risk factor in several foodborne disease outbreaks. However, the use of microwave ovens in restaurants and other food service establishments has not been well documented. The aim of this study was to describe the types of food service establishments that use microwave ovens, how these ovens are used, types of foods heated or cooked in these ovens, types of microwave ovens used in food service establishments, and the level of compliance with U.S. Food and Drug Administration (FDA) guidelines. From 2008 to 2009, the Minnesota Department of Health collected data from a convenience sample of 60 food establishments within the state. Facility types included fast-food restaurants, sit-down restaurants, school food service, nursing homes, hotels and motels, and daycare centers. Food preparation practices were classified as prep-serve, cook-serve, or complex. Minnesota environmental health specialists administered a study questionnaire to managers during routine inspections. Establishments included in this study reported using microwave ovens primarily to warm commercial ready-to-eat products (67%) and to warm foods for palatability (50%). No minimum temperatures are required for these processes because these foods do not require pathogen destruction. However, food establishments using complex preparation practices more often reported using microwave ovens for multiple processes and for processes that require pathogen destruction. For establishments that did report microwave oven use for food requiring pathogen destruction, the majority of managers reported following most FDA recommendations for cooking and reheating for hot-holding potentially hazardous foods, but many did not report letting food stand for 2 min after cooking. Additional training on stand time after microwave cooking could be beneficial because of low reporting of this practice among study participants.