OBJECTIVE The maintenance of stromal hydration by the corneal endothelium relies on active transendothelial anion transport, with bicarbonate and chloride the major anions carrying the current. However, the ion transport pathways that operate to maintain stromal hydration have yet to be fully elucidated. METHODS We used RT-PCR to identify the gene expression profile of members of the ClC family of chloride channels in freshly isolated samples of rabbit corneal endothelium, stroma, and epithelium. The expression of a separate group of genes was also examined to confirm the purity of the sample collection protocol. The expression of the ClC-2 and ClC-3 channel protein in the cornea was also evaluated by light and electron microscopic immunolabelling. RESULTS The mRNA for ClC-2, ClC-3, ClC-5, ClC-6, and ClC-7 were expressed in both the corneal epithelium and endothelium, and in the stroma. The mRNA for the skeletal muscle specific channel ClC-1 and the kidney specific chloride channel ClC-Ka were not detectable. ClC-4 mRNA was not detected in any rabbit tissue examined. The expression pattern of the mRNAs for collagens V, VI, VII, and VIII demonstrated the absence of contamination in epithelial and endothelial samples. ClC-2 and ClC-3 immunolabelling confirmed the presence of these proteins in corneal endothelium, stroma, and epithelium. CONCLUSIONS Together with cystic fibrosis transmembrane conductance regulator (CFTR) and calcium activated chloride channel-1 (CLCA1), these results bring the number of chloride channel genes known to be expressed in the corneal endothelium and epithelium to seven. These channels are likely to be important for the maintenance of corneal transparency.