During a critical period in its postnatal development the mammalian visual cortex displays susceptibility to experience-dependent alterations of neuronal response properties. Plasticity represents an integrated set of developmental processes controlled by a transcriptional hierarchy that coordinates the action of many genes. To illuminate the expression of these critical genes, we examined gene expression patterns of 18371 non-redundant cDNAs in the visual cortex of cats at birth, at eye opening, at the peak of the critical period of eye dominance plasticity and in the adult cat using filter-based cDNA arrays and software-based hierarchical cluster analysis. We identified a small set of genes that were selectively expressed during the peak of the critical period for plasticity. We further examined the patterns of expression of these genes by analyzing the gene expression pattern of dark-reared chronologically older animals that are known to retain this ocular dominance plasticity beyond the chronologically defined critical period. This additional cluster assessment allowed us to separate age-related changes in the patterns of gene expression from plasticity-related changes, thus identifying a subset of genes that we define as plasticity candidate genes. Those plasticity candidate genes that have previously characterized functions include participants in second messenger systems, in cell adhesion, in transmitter recycling and cytokines, among others. Comparison of cDNA array quantitation with reverse transcription-polymerase chain reaction showed almost identical expression profiles for three genes that we examined. The expression pattern of one identified gene, opioid binding cell adhesion molecule, from the cDNA array analysis, is also in agreement with immunocytochemical results. We conclude that the approach of high-density cDNA array hybridization can be used as a useful tool for examining a complex phenomenon of developmental plasticity since it is amenable to multiple developmental stage gene expression comparisons.