BACKGROUND Collagen has effects on cell morphology, differentiation characteristics and function. Using collagen gel culture, several studies about cell differentiation were reported. In this study, the differentiation of rabbit conjunctival epithelial cells in a collagen gel-embedding culture system was investigated by electron microscope and lectin labeling. METHODS Rabbit bulbar conjunctival epithelial cells were cultured in type I collagen gel. After 1 and 2 weeks of culture, some of these cells were stained with PAS and seven kinds of lectins, and others were examined by transmission electron microscopy. RESULTS The conjunctival epithelial cells cultured within collagen gel formed stratified cell layers and globules with cavities. The inner layer cells facing the cavities showed PAS and lectin staining patterns similar to those of conjunctival goblet cells in vivo, whereas the staining patterns of the outer layer cells on the collagen matrices resembled the patterns of non-goblet epithelial cells. Microvilli on the surface of the innermost cells, basement membranes beneath the outermost cells, tight junctions, adherent junctions, interdigitating folds and desmosomes between cells were identified on electron microscopic examination. CONCLUSIONS These results indicate that cell junction structures of the conjunctival epithelial cells are well developed in collagen gel-embedding culture systems, and that the inner layer cells have carbohydrates similar to those of conjunctival goblet cells. Culture of conjunctival epithelial cells within collagen gel is a useful model for examining differentiation of these cells.