The junctional epithelium surrounds the tooth. It is composed of stratified squamous non-keratinized epithelium. It is attached on one surface by the tooth and on another one to the gingival connective tissue. It is composed of the internal basal lamina or suprabasal layer, which extends to the tooth surface, and of the external basal lamina or basal layer, which faces the connective tissue. The junctional epithelium forms when the reduced enamel epithelium still lines most of the crown surface and it is eventually remodeled into the junctional epithelium. It extends from the base of the gingival sulcus to approximately 2 mm coronal to the alveolar bone crest. The attachment of the junctional epithelium to the tooth is mediated through the epithelial attachment apparatus. This consists of hemidesmosomes at the plasma membrane of the cells directly attached to the tooth (DAT) and the basal lamina on the tooth surface. The density of the intercellular junctions is less than that observed in the mouth, which makes it more susceptible to mechanical disruptions.

The functions of the junctional epithelium are first to form an epithelial barrier against plaque and bacteria. Secondly, to allow access of the gingival crevicular fluid, inflammatory cells and components of the host’s defenses to the gingival margin. Thirdly, the cells exhibit a rapid turnover, which contributes to the rapid repair of damaged tissue and equilibrium of parasites. During disease, the junctional epithelium allows the emigration of polymorphonuclear cells and the migration of microorganisms from bacterial plaque and associated toxins to enter the tissue. This process results in acute inflammation and epithelial ulceration, which allows the damaging agents to penetrate deeper into the periodontium. In addition, the gingival crevicular fluid that passes through the junctional epithelium provides the nutrients necessary for the directly attached to the tooth cells to grow. During health, the amount of gingival crevicular fluid is minute, but during inflammation the amount present increases and it becomes something resembling an inflammatory exudate.

The junctional epithelium is the first line of defense against microbial invasion in tissue. Even though it provides a barrier many substances such as lipopolysaccharides pass through, but have only limited access since both the internal and external basal layers act as barriers. Another aspect of the defense mechanism is the rapid turnover, which provides an effective removal of bacterial clinging to the epithelial cells. Moreover, the junctional epithelium has enzyme rich lysosomes such as matrilysin, cathepsin and alpha defensing. In addition, the junctional epithelium cell surface receptors respond to extracellular molecular changes by producing intracellular adhesion molecules (ICAM), and chemotactic substances such as C5a, leukotriene B-4 and IL-8. 

Continued exposure of the junctional epithelium to bacterial challenges may lead to subgingival plaque formation, transformation of the gingival sulcus into a periodontal pocket, and an increase in the inflammatory focus in the connective tissue. The consequences stated are reasons to encourage the understanding of this structure of the oral environment and to encourage the maintenance of oral health.