Technical Abstract: Among dietary phytonutrients, carvacrol, cinnamaldehyde, and Capsicum oleoresin are well-known for their anti-inflammatory and antibiotic effects in human and veterinary medicine. To further define the molecular and genetic mechanisms responsible for these properties, broiler chickens were fed a standard diet supplemented with either of the three phytochemicals and intestinal intraepithelial lymphocytes were examined for changes in gene expression by microarray analysis. When compared with chickens fed a non-supplemented standard diet, carvacrol-fed chickens showed altered expression of 74 genes (26 up-regulated, 48 down-regulated) and cinnamaldehyde led to changes in the levels of mRNAs corresponding to 62 genes (31 up-regulated, 31 down-regulated). Most changes in gene expression were seen in the Capsicum-fed broilers with 98 up-regulated and 156 down-regulated genes compared with untreated controls. Results from the microarray analysis were confirmed by quantitative real-time PCR with a subset of selected genes. Among the genes which showed >2.0-fold altered mRNA levels, most were associated with metabolic pathways. In particular, with the genes altered by Capsicum oleoresin, the highest scored molecular network included genes associated with lipid metabolism, small molecule biochemistry, and cancer. In conclusion, this study provides a foundation to further investigate specific chicken genes that are expressed in response to a diet containing carvacrol, cinnamaldehyde, or Capsicum oleoresin.