Modern broiler chickens have been selected for rapid growth and optimal food efficiency. Comparing modern and heritage broiler lines provides insight into the changes that have occurred during human directed selection. Previous work comparing Ross708 and a Heritage line maintained at the University of Illinois revealed significant differences in intestinal growth. In particular, when normalized for the size of the bird, Ross708 birds have longer jejunal and ileal segments than the Heritage birds. More recently, we have shown that although the duodenum lengths are similar, the Ross birds have longer duodenal villi than the Heritage birds. These intestinal segment differences could support the modern broilers need for increased nutrient absorption. In this study, we have analyzed gene expression patterns from Ross708 and Heritage duodenal samples. Transcriptome libraries were generated from these tissues using the Illumina TruSeq RNA sample prep kit with sequencing yielding over 5 million tags per sample. Comparing gene expression levels between the two lines reveals differences in genes affecting translation, extracellular matrix interactions and kinase mediated signaling. These data should provide insight into the how human directed evolution has affected gene expression levels in these lines of chickens.