It is becoming clear that Hox genes, which encode transcription factors of the Antennapedia homeodomain family, are key players in establishing the body plan of mammalian embryos. They have already been implicated in the formation of the central nervous system, tissues derived from neural crest, the vertebral column and the limbs. In order to examine the roles of hoxa-4 and hoxa-6 during development, mice with targeted disruptions in these genes were generated. Each shows homeotic transformation of cervical vertebrae, at positions that approximate the anterior borders of expression of these genes in the prevertebrae. Defects were not observed in other tissues that normally express these genes. Hoxa-4-/hoxa-4- mice show, with 100% penetrance, anterior transformations of the dorsal aspects of the third cervical vertebra by acquiring features normally associated with the second cervical vertebra. Mice homozygous for the hoxa-6 mutation show, with incomplete penetrance, even on opposite sides of the same animal, posterior transformations of the seventh cervical vertebra to the first thoracic vertebra. In addition, both hoxa-4-/hoxa-4- and hoxa-6-/hoxa-6- mice show variability in expressivity. These data indicate that alternative genetic pathways can partially, and at times completely, substitute for the function of these two genes. Other members of these two paralogous Hox families are good candidates for providing the substitutions. As paralogous genes lie on different chromosomes, it is possible to examine the degree of redundancy among these genes by intercrossing mice with the appropriate individual disruptions. The analysis of double, triple and even quadruple mutants should determine the ways in which these Hox genes interact in order to specify the multitude of tissues in a restricted region of the developing mouse embryo.