Genetic gain in the yield of modern maize reflects increased stress tolerance. The manipulation of genes for deliberate alterations in tolerance relies on an understanding of the regulation and components of stress responses. Transcriptome analysis of an ultraviolet (UV) radiation time course with paired treatment and control measurements yielded groups of coordinately regulated genes and gene ontology processes. A comparison of the patterns of gene expression with patterns of morphological changes allowed the identification of physiologically relevant gene expression regulons. A set of genes significantly affected by UV radiation in maize leaves was selected by linear modelling plus order-restricted inference profile matches. This gene list was used to find upstream sequence motifs that predict the UV regulation of maize gene expression.