DNA arrays can be used to simultaneously analyze the expression of hundreds of genes and permit systematic approaches to biological discovery with a potentially profound impact on genomics, pharmacogenomics, and proteomics. Microarrays have been used to study host-pathogen interactions, and recently this technology has been applied to investigate host-virus interactions. DNA arrays are used to monitor host alterations in several virus-induced cancers and upon infection with wild-type or modified viruses, or viral gene products. Alternatively, viral chips are used to characterize the transcriptional program of pathogenic viruses and in antiviral drug screening and drug resistance. With an aim to extend the use of this technology to ocular research, and specifically to study changes in host cell transcription in ocular adenovirus infection, we used a commercial array to compare adenovirus-infected human corneal cells to mock-infected cells. Of the 1176 genes analyzed, 72 genes associated with cell cycle regulation, apoptosis, oncogenesis, transcription, signaling, and inflammation were differentially regulated. In this review we summarize the use of DNA arrays in the study of viral infections and suggest potential uses of the technology in ocular viral pathogenesis research.