The retinal pigment epithelium (RPE) is a monolayer of cuboidal cells that lies in close association with the rod and cone photoreceptors and is thought to play an important role in setting up ion gradients within the interphotoreceptor matrix. Although electrophysiological recordings have permitted a rudimentary analysis of ion channel classes contributing to ionic movements across the RPE, little is known about the channel subtypes expressed in this tissue. In the present study we have used cDNA microarray technology to provide a more comprehensive overview of ion channel expression in both mature and proliferating human RPE cells.Total RNA was isolated from ARPE-19 cells after 1-mo (mature) or 4-d (proliferating) in culture. RNA was reversed transcribed and hybridised to cDNA microarrays containing 12,000 expressed human sequences (Agilent, human 1). Fluorescent labelling was performed with a 3DNA SubMicro kit (Genisphere) and spot intensities were measured using ScanAlyze (Stanford Computer Graphics Laboratory Freeware). Ion channel data was extracted from the microarrays using VectorXpression software (Informax) in conjunction with a purpose-built database (Microsoft Excel) comprising Genbank accession and Unigene numbers for all known α subunits of human ion channel genes.The ion channel database contained 252 ion channels, of which 137 were represented on the human microarrays. Based on replicate arrays, the same group of ion channels were found to be highly expressed in both mature and proliferating RPE. For example, six channels were found to be among the most highly expressed in both groups. Of these, an inward rectifier potassium channel (KCNJ13) and a chloride channel (CLCN1) have been previously characterised in RPE. The remaining four channels, a gap junction channel protein (GJA1), a gamma-aminobutyric acid receptor (GABAR1), a polycystic kidney disease cation channel (PKD2) and a voltage dependent anion channel (VDAC1) have not been previously identified. This study has demonstrated the use of cDNA microarrays for the rapid profiling of ion channel subtype expression in human RPE cells. Evidence has been obtained for the presence of previously uncharacterised channels and their functional significance now warrants further investigation. Overall, mature and proliferating RPE cells appear to display similar ion channel expression profiles.