Mice homozygous for a targeted mutation of the Hoxa-2 (Hox 1.11) gene are born with cleft palates and die within 24 hr of birth. Analysis of stained skeletons revealed that homozygous mutant animals contained multiple cranial skeletal defects, including a duplication of the ossification centers of the bones of the middle ear. Histological analysis suggested that this duplication resulted from the transformation of skeletal elements derived from the second branchial arch into more anterior structures, resulting in a duplication of Meckel's cartilage adjacent to the otic capsule. Skeletal elements normally derived from the second arch were absent in the mutants. These data provide direct experimental evidence for the existence of a branchial Hox code.