The adult vertebrate hind brain regulates critical body functions such as sleep, respiration and heart rate. During embryogenesis, the hindbrain forms seven transient swellings called rhombomeres, each with distinct morphology and gene expression patterns. Rhombomere specification and regulation is controlled by transcription factors including members of the Hox family and Krox20. Disruption of these genes changes the number and properties of rhombomeres and leads to neuronal disorganization causing animal lethality. We are using transcriptional profiling and functional validation to reveal rhombornere specific patterns of gene expression regulated by these key transcription factors. We isolated individual rhombomeres from 9.5 dpc mouse embryos using laser capture microscopy and performed transcriptional profiling on either single rhomborneres from wild type hindbrains or whole hindbrains of wild type and Hoxa1, Hoxa2, Hoxb1 and Krox20 mutants. Analyses and validation of these results have uncovered several novel targets and pathways associated with hindbrain specification. For example, Hox genes which are induced by retinoids in turn modulate retinoid metabolism. These feedback loops are important for hindbrain patterning. We also discovered rhombomere-specific genes, genes involved in neurogenesis in the hind brain along with the downstream targets of Hoxa1, Hoxa2, Hoxb1 and Krox20.