Mesenchyme-derived instructions for odontogenic epithelial differentiation into ameloblasts and the production of enamel matrix has been well established. However, it is not known how position-specific differences within the enamel organ of rodent molar tooth organs regulate the enamel-forming vs. the enamel free areas in the developing cusp. Light microscopy, transmission electron microscopy, and immunocytochemistry using a rabbit anti-mouse amelogenin antibody, were used to map the position-specific patterns within the enamel organ. In the enamel-forming area, ameloblasts were associated with stratum intermedium. In the enamel-free area, another cell type was interposed between inner enamel epithelia (IEE) and stratum intermedium. IEE in the enamel-free area did not have Tomes' processes and secreted enamel matrix not only toward dentin but also between IEE cells. IEE became confluent with stellate reticulum; at this position stratum intermedium cells were no longer detected. The thickness and orientation of dentin matrix collagen fibers in the enamel-free area were different from the fibers in the enamel-forming area. These results suggest that the patterns of epithelial cell-cell and cell-matrix associations during position-specific enamel organ epithelial differentiation may regulate ameloblast matrix synthesis and/or the matrix secretion pathway.