Both the endogenous commensal flora and a dysregulated mucosal immune response have been implicated as contributing to the pathogenesis of human intestinal disease. Unmethylated cytosine-guanine (CpG)-containing DNA, the ligand for Toll-like receptor 9 (TLR9), is a recently recognized microbial product with immunostimulatory and immunoregulatory effects. TLR9 is expressed by many cell types located in the intestine, including epithelial cells and classical immune cells. The physiological impact of the juxtaposition of these factors (bacterial DNA and responsive cells) in the gut therefore bears consideration. Here we discuss studies that examine the interaction between CpG DNA and the intestine, focusing on activation of epithelial cells, administration of CpG-containing oligonucleotides as therapy for experimental inflammatory enteropathies, and the role of CpG DNA in mediating the beneficial effects of bacterial probiotics.