The bagpipe-related homeobox-containing genes are members of the NK family, bagpipe (bap) was first identified in Drosophila and there are three different bagpipe-related genes in vertebrates. Only two of these are found in mammals, the Nkx3.1 and the Bapxl (Nkx3.2) gene. The targeted mutation in the mouse Bapxl gene shows a vertebral phenotype in which the ventromedial elements are lacking; these are the centra and the intervertebral discs. In addition, a region of gastric mesenchyme is abnormal. This mesenchyme surrounds the posterior region of the presumptive stomach and duodenum, and in the mutant fails to support normal development of the spleen. In Drosophila, bagpipe has a role in gut mesoderm and the mutant embryos have no midgut musculature. Thus bap related genes in mouse and Drosophila have roles in patterning gut mesoderm; however, neither of the mammalian genes has a discernible role in the gut musculature. In contrast, both mammalian genes have roles in developmental processes that have appeared recently in evolution. The Bapxl gene found in fish, amphibians, birds and mammals appears to have derived vertebrate specific functions sometime after the split between the jawless fish and gnathostomes.