At the cusp tip of rodent molar, there is a region of dentin without an enamel cap. This region is called enamel free area (EFA). The surface collagen arrangement has been reported to differ between the EFA and the dentin covered with the enamel (DCE). To clarify the cause of this difference, we observed the ultrastructure of the basement membrane and the distal ends of the inner enamel epithelium (IEE) in rats. At 20 days prenatal, distal ends of IEE were relatively flat on both the DCE and EFA. Ultrastructurally, there was no difference between the basement membranes. At newborn, no marked changes were observed in the morphology of the distal end of IEE on the DCE or the EFA, but aperiodic microfibrils perpendicular to basal lamina were denser and longer on the DCE than the EFA. At 2 days postnatal, cytoplasmic extensions from distal end of IEE penetrated through basal lamina, and these extensions were more developed on the DCE than the EFA. On the DCE, collagen fibrils ran into and between cytoplasmic extensions and were arranged perpendicular to the surface. On the EFA, collagen fibrils ran parallel to the surface, and few collagen fibrils ran into and between cytoplasmic extensions. These findings suggested that the differences in the collagen arrangement between the EFA and DCE are associated with the developmental state of aperiodic microfibrils in the basal lamina beneath IEE and the morphology of the distal end of IEE.