Most of the current knowledge on mechanisms underlying Shigella pathogenesis is derived from studies of S. flexneri. Infection with the invasive pathogen S. flexneri is a multistep process (Fig. (Fig.1).1). To gain access to the intestinal mucosa, S. flexneri crosses the intestinal epithelium, which evolved as a physical and functional barrier to protect the body against the invasion of commensal and pathogenic bacteria (249). In the initial phase of infection, S. flexneri apparently does not invade the epithelial barrier from the apical side but instead triggers its uptake into microfold cells (M cells) and is transcytosed across the epithelial layer (250, 325). M cells are specialized epithelial cells (EC), which continuously sample particles from the gut lumen and deliver them to the underlying mucosal lymphoid tissue, where immune responses can be initiated (157). The use of M cells as an entry port is consistent with the in vitro observation that S. flexneri barely interacts with the apical surface of polarized EC and enters these cells preferentially through the basolateral pole (179).