Epithelial cells at all mucosal surfaces are potentially apposed to bacteria, particularly in the intestine. It is established that intestinal epithelial cells (IECs) represent an important barrier between lamina propria cells and the potentially harmful lumenal contents. In addition, IECs are important immunoeffector cells with the capacity to release cytokines, chemokines, and other molecules involved in antigen presentation and immune defense. The interaction of IECs with intestinal bacteria can result in a decrease in barrier function and the development of inflammation, which is known to be an important factor in the development of intestinal pathology. The potential role of such crosstalk between bacteria and other intestinal cell types in normal physiology and/or pathophysiology is therefore a topic of intense investigation. In this chapter, we provide protocols for the identification of bacteria that are associated with the epithelium and mucosa in addition to functional assays examining the interactions of neutrophils with epithelial cells and epithelial cell-mediated killing of bacteria.