E. coli O157:H7 is an important foodborne pathogen, and ground beef is a common vehicle of infection. DNA microarrays have been used for transcriptomic studies of E. coli O157:H7 using laboratory media; however, analysis of gene expression in complex matrices such as food are lacking. This study compared gene expression profiles of E. coli O157:H7 Sakai strain in raw ground beef extract (GBE) and tryptic soy broth (TSB). Total RNA was isolated from GBE and TSB after 2 h of incubation with E. coli O157:H7. Following reverse transcription (RT) of the RNA, labeled cDNA was hybridized to microarrays representing 9608 open reading frames (Operon; Genome Array-Ready Oligo Set) corresponding to 4 genomes of E. coli strains and 3 plasmids. There were 74 up-regulated (genes involved in protein and polysaccharide biosynthesis, transcription factors, membrane transport proteins, and acid shock proteins) and 54 down-regulated (encoding proteins for energy metabolism, biosynthesis of cofactors, transporters of small molecules, and transcription factors and enzymes responsible for protein degradation) genes in E. coli O157:H7 grown in GBE compared to TSB, respectively. Furthermore, compared to incubation in TSB, E. coli O157:H7 incubated in GBE for 2 h showed significantly increased survival when exposed to synthetic gastric fluid, pH 1.5. This study demonstrated that microarray analyses can be performed using complex food matrices, and gene expression of E. coli O157:H7 differs in TSB compared to GBE. The information will be useful for identification of genes that can be employed as potential targets for interventions to control E. coli O157:H7.