The microarray is a revolutionary technology combining molecular biology and computer technology in the high throughput, simultaneous analysis of global gene expression. It is emerging as a powerful and valuable research tool that holds great promise in elucidating the molecular mechanisms involved in complex diseases. The information gained may provide direction toward identifying appropriate targets for therapeutic intervention. Despite the enormous potential of this technology, however, a number of issues exist that complicate gene expression analysis and require further resolution. This paper reviews these issues as well as the conceptual, practical and statistical aspects of microarray technology, including its current use in research and clinical applications. Furthermore, the advantages and potential benefits of this technology in ophthalmic research are discussed, with particular attention to retinal diseases, and its possible application in the identification of genes involved in ocular disease progression that may serve as clinical markers or potential therapeutic targets.