While the gut epithelium represents the largest mucosal tissue, the mechanisms underlying the interaction between intestinal bacteria and the host epithelium lead to multiple outcomes that remain poorly understood at the molecular level. Deciphering such events may provide valuable information as to the mode of action of commensal and probiotic microorganisms in the gastrointestinal environment. Potential roles of such microorganisms along the privileged target represented by the intestinal immune system include maturation processes prior, during and after weaning, and the reduction of inflammatory reactions in pathogenic conditions. As commensal bacteria are naturally coated by natural and antigen-specific SIgA in the gut lumen, understanding the consequences of such an interaction may provide new clues on how the antibody contributes to homeostasis at mucosal surfaces. This review discusses several aspects of the role of SIgA in the essential communication existing between the host epithelium and members of its microbiota.