HOX genes play a fundamental role in the development of the vertebrate central nervous system, heart, axial skeleton, limbs, gut, urogenital tract and external genitalia. The homeobox gene Hoxb-1 is critical to hindbrain development and has phenotypic features frequently observed in autism. Analysis of expression and targeted disruption of Hoxb-1 demonstrates that it is also essential for patterning progenitor cells along the entire DV axis of rhombomere 4 (r4). Hoxb-1 maintains this function by acting very early during hindbrain neurogenesis to specify effectors of the sonic hedgehog and Mash1 signaling pathways. Hoxb2 is a homeodomain protein important in neural development that is also expressed during erythropoiesis, hindbrain development and normal human adult lung development. Hoxb2 may modulate the amount of gamma-globin mRNA expressed during development and differentiation. In addition, Hoxb2 plays an important role in the patterning of hindbrain and pharyngeal arches in the zebrafish.