The expression of four different gap junction (GJ) transcripts, corresponding to the alpha-1, alpha-3, beta-1 and beta-2 gene products, has been examined in the ciliary epithelium of human and bovine eyes, and in cultures of ciliary epithelial cells. Northern blot analysis revealed that alpha-1 mRNA, 3.6-kb in size, was the predominant transcript expressed in intact tissue and in cultures of pigmented ciliary epithelial cells (PE). No transcripts from the alpha-3, beta-1 or beta-2 gap junction genes were detected in intact tissue or ciliary epithelial cells as demonstrated by Northern blotting. When the levels of alpha-1 gap junction mRNA were compared between PE and NPE in primary cultures, a striking difference was observed in the level of alpha-1 transcripts: there was about a 6 to 8-fold increase in alpha-1 levels in PE cells, relative to the NPE cells. To verify the differential level of expression of alpha-1 GJ mRNA in the two cell types, indirect immunofluorescence localization studies were performed on semithin cryostat sections of ciliary processes. These studies revealed that alpha-1 gap junctions are present at the apical and lateral borders of PE cells, i.e. at the apical plasma membranes domains of PE-NPE cells, and at the lateral plasma membrane regions of PE-PE cells borders. Further analysis by immunoblotting confirmed that the 43 kD alpha-1 gap junction protein was the major gap junction gene product in the ciliary epithelium.