The current model to explain the organization of the mammalian nervous system is based on studies of anatomy, embryology, and evolution. To further investigate the molecular organization of the adult mammalian brain, we have built a gene expression-based brain map. We measured gene expression patterns for 24 neural tissues covering the mouse central nervous system and found, surprisingly, that the adult brain bears a transcriptional ''imprint'' consistent with both embryological origins and classic evolutionary relationships. Embryonic cellular position along the anteriorposterior axis of the neural tube was shown to be closely associated with, and possibly a determinant of, the gene expression patterns in adult structures. We also observed a significant number of embryonic patterning and homeobox genes with region-specific expression in the adult nervous system. The relationships between global expression patterns for different anatomical regions and the nature of the observed region-specific genes suggest that the adult brain retains a degree of overall gene expression established during embryogenesis that is important for regional specificity and the functional relationships between regions in the adult. The complete collection of extensively annotated gene expression data along with data mining and visualization tools have been made available on a publicly accessible web site (www.barlow-lockhartbrainmapnimhgrant.org).database ͉ development ͉ evolution ͉ gene expression profiling ͉ inbred strains of mice T he adult nervous system achieves its mature form as the result of neuroectodermal cells committing to a specific fate and then segregating into distinct regional collectives of neurons that become fully functional through establishment of connections to other neurons. Our current understanding of brain architecture and organization is based on studies of embryology, anatomy, and evolution in which direct observation of anatomic structures was the foundation for postulated models of brain structure (1). Recent models of brain development and maturation consider relationships between different regions based on the expression of specific genes in assigning developmental origins of adult structures (2, 3). Here, we have constructed a regional gene expression atlas of the adult mouse brain and analyzed the quantitative results by using molecular classification algorithms.Genome-wide gene expression profiling is a powerful technique for deriving information about specific brain regions (4, 5). This approach has been used to measure gene expression patterns in particular regions, subregions, or cell populations in the brain (6-11). Two previous studies have analyzed gene expression differences across multiple regions of the mammalian brain by using multiple strains or species (12,13). However, the current study is the most extensive to date in terms of the number of genes and the coverage of different neural tissues. Our goal was to create a publicly accessible gene-based brain map with data sets, metadata, datab...