The expression of four different gap junction (GJ) transcripts, corresponding to theα1,α3,β1 andβ2 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 oq 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 theα3,β1 orβ2 gap junction genes were detected in intact tissue or ciliary epithelial cells as demonstrated by Northern blotting. When the levels ofαgap junction mRNA were compared between PE and NPE in primary cultures, a striking difference was observed in the level of ai transcripts: there was about a 6 to 8-fold increase inα1 levels in PE cells, relative to the NPE cells. To verify the differential level of expression of ai GJ mRNA in the two cell types, indirect immunofluorescence localization studies were performed on semithin cryostat sections of ciliary processes. These studies revealed that al 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 ai gap junction protein was the major gap junction gene product in the ciliary eoithelium.