Maize is an important model species and a major constituent of human and animal diets. It has also emerged as a potential feedstock and model system for bioenergy research due to recent worldwide interest in developing plant biomass-based, carbon-neutral liquid fuels. To understand how the underlying genome sequence results in specific plant phenotypes, information on the temporal and spatial transcription patterns of genes is crucial. Here we present a comprehensive atlas of global transcription profiles across developmental stages and plant organs. We used a NimbleGen microarray containing 80 301 probe sets to profile transcription patterns in 60 distinct tissues representing 11 major organ systems of inbred line B73. Of the 30 892 probe sets representing the filtered B73 gene models, 91.4% were expressed in at least one tissue. Interestingly, 44.5% of the probe sets were expressed in all tissues, indicating a substantial overlap of gene expression among plant organs. Clustering of maize tissues based on global gene expression profiles resulted in formation of groups of biologically related tissues. We utilized this dataset to examine the expression of genes that encode enzymes in the lignin biosynthetic pathway, and found that expansion of distinct gene families was accompanied by divergent, tissue-specific transcription patterns of the paralogs. This comprehensive expression atlas represents a valuable resource for gene discovery and functional characterization in maize.