Shigella are Gram-negative bacteria which cause diarrhea. Shigella consist of four species, with S. flexneri serotype 2a, S. sonnei, and S. dysenteriae type 1 being significant causes of disease. Shigella infection annually kills greater than 600,000 children under the age of five in developing countries, and there is no vaccine. S. flexneri causes 60% of Shigella infections in developing countries. By comparing in vivo and in vitro gene expression of S. flexneri 2a 2457T by microarray and performing genomic comparison, genes that were both differentially expressed during intracellular growth and specific to S. flexneri were identified. One gene, now named icgR, had decreased intracellular expression and was chosen for further characterization. Deletion of icgR, a previously uncharacterized DeoR family transcriptional regulator, lead to increased intracellular replication. RNAseq analysis of ΔicgR and wild type bacteria demonstrated increased expression of 176 genes and decreased expression of 65 genes in vitro and increased expression of 500 genes and decreased expression of 378 genes in vivo. Of particular interest was the increased expression of the branched-chain amino acid transporter encoded by the liv operon observed in both growth conditions. These transporters have previously been shown to be important for in vivo growth and pathogenesis in other bacteria and may be responsible for the increased intracellular replication seen in the ΔicgR mutant. In addition to studying genes unique to S. flexneri, the expression of genes that are conserved between S. flexneri 2a 2457T, S. sonnei 53G, and S. dysenteriae type 1 1617, was measured by RNAseq. There were 114 conserved genes with increased intracellular expression including multiple global transcriptional regulators such as hns and fur. There were also 196 conserved genes with decreased intracellular expression including the genes for amino acid biosynthesis. Additionally, there were 3 genes uncharacterized genes that were conserved, exhibited increased intracellular expression, and were predicted to be located at the cell surface. These genes may be novel targets for a global vaccine. This study represents a global view of Shigella transcriptional activity in the intracellular environment and provides a foundation for discovery of new regulatory pathways and novel vaccine targets.