In the intestine, multiple interactions occur with the external world. Thus, the intestinal mucosal barrier has to tolerate millions of microorganisms that commonly inhabit the gut, degrade and absorb food, and establish tolerance or immunity, depending on the nature of the encountered antigens. Recent findings have highlighted that intestinal epithelial cells are not simply a barrier, but also are crucial for integrating these external and internal signals and for coordinating the ensuing immune response. Here, I review these findings and show how epithelial cells harmonize information that comes from inflammatory and non-inflammatory components of the microbiota to preserve intestinal homeostasis. If dysregulated, this immunomodulatory function of epithelial cells might contribute to the development of intestinal inflammation.