The intestinal epithelia proliferate and differentiate along the crypt villus axis to constitute a barrier cell layer separating some 10¹³ potentially harmful bacteria from a sterile mucosal compartment. Strict regulatory mechanisms are required to maintain a balance between the appropriate uptake of luminal food components and proteins, while constraining the exposure of the mucosal compartment to luminal antigens and microbes. The enteric nervous system is increasingly recognized as such a regulatory housekeeper of the epithelial barrier integrity, in addition to its ascribed immunomodulatory potential. Inflammation affects both epithelial integrity and barrier function and, in turn, loss of barrier function perpetuates inflammatory conditions. The observation that inflammatory conditions affect enteric neurons may add to the dysregulated barrier function in chronic disease. Here, we review the current understanding of the regulatory role of the nervous system in the maintenance of barrier function in healthy state, or during pathological conditions of, for instance, stress-induced colitis, surgical trauma or inflammation. We will discuss the clinical potential for advances in understanding the role of the enteric nervous system in this important phenomenon.