This review summarizes the biological properties of the junctional epithelium, focusing on its developmental aspects, wide intercellular spaces and desmosomes, dense granules, permeability barrier, phagocytotic activity, adhesive structures and nerve terminals. It also discusses the morphology and functions of long junctional epithelium and peri-implant epithelium. Junctional epithelium is derived from the reduced enamel epithelium during tooth development. Apoptosis occurs in the border between oral and reduced enamel epithelia during tooth eruption. Junctional epithelium expresses a cytokeratin-19 immunoreaction, suggesting that this protein is a consistent differentiation marker. Wide intercellular spaces, which contain neutrophils and nerve endings, are formed as there are fewer desmosomes than in the oral epithelium. Dense, membrane-bound granules in the epithelium might correspond with membrane-coating granules, as revealed by their shape, components and freeze-fracture images. Junctional epithelium with high permeability contains exogenously expressed alpha-defensins, while stratified epithelia contain endogenously expressed beta-defensins. The phagocytotic activity in this epithelium remains unclear. Integrin-alpha6beta4 and laminin-5 form a complex in the tooth surface internal basal lamina. Long junctional epithelium created experimentally attaches to the cementum surface by hemidesmosomes and basal lamina. The peri-implant epithelium differs in proliferation and in adhesive structure from the normal junctional epithelium. In conclusion, wide intercellular spaces and poorly developed desmosomes are closely correlated with a permeable nature. There is still uncertainty over the phagocytotic activity of the epithelium. Integrin-alpha6beta4 and laminin-5 form a significant complex in the internal basal lamina. Junctional epithelium receives a rich sensory nerve and has a high rate of cell turnover. Long junctional epithelium can be produced rapidly during wound healing, due to high proliferative activity. Peri-implant epithelium might be a poorly adhered and permeable epithelium.