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More than 90% of elementary school students in Korea have lunch provided by a school feeding program. This study examined nonheated foods, foods in which final ingredients were added after cooking ("heated/nonheated foods"), and desserts for microbial contamination levels and the presence of foodborne pathogens. We obtained a total of 77 food samples belonging to the above three groups from four elementary schools located in Iksan, Jeonbuk, Korea, from June to July 2010. Among the samples, 15% of nonheated foods and 9% of heated/nonheated foods contained > 6 log CFU of aerobic bacteria per g. Unacceptable coliform counts according to Korean national standards (3 log CFU/g) were also observed in 30, 4.5, and 26% of nonheated foods, heated/nonheated foods, and desserts, respectively. The foodborne pathogens Escherichia coli O157:H7, Bacillus cereus, and Cronobacter sakazakii were found in two, one, and two of the total samples, respectively. Detection of E. coli O157:H7 indicates a low level of safety in the school lunches served in Korean elementary schools. To improve food safety, hazard analysis critical control point guidelines should be applied to school food service establishments to lower the microbial risks in foods served to children.