Besides its important role of digestion and absorption, esophageal tissue has an essential role as a major barrier against intraluminal pathogens like hostile microorganisms and toxins. This barrier function is achieved via various mechanical, chemical, and immunological mechanisms which are typically altered in inflammatory diseases, thereby causing subsequent damage of the mucosa. In this review we will focus on the main structural and functional barriers of host defense within the esophageal mucosa, including the epithelial layer, membrane-bound and secretory mucins, and different types of defensins. In addition, we will discuss the relevance of biofilm on esophageal tissue and will illustrate the importance of different regulators of intestinal permeability like zonulin and desmosomal components.