Rapid enumeration of Escherichia coli strains by quantitative real-time PCR targeting the uidA gene was developed and confirmed for minced beef, tuna and raw oyster. Higher sensitivity (1 CFU/g of E. coli in all three food samples) was obtained by incubating for 7 h in TSB. Colony-directed E. coli specific TaqMan PCR assay could effectively distinguish colonies grown on various selective media within 1.5-h. Inspection of E. coli in food testing laboratories is important, and our rapid E. coli detection strategy will contribute to quality control in food industries.