Segmentation of the vertebrate hindbrain into rhombomeres is important for the anterior-posterior arrangement of cranial motor nuclei and efferent nerves. Underlying this reiterated organization, Hox genes display segmentally restricted domains of expression, such as expression of Hoxb-1 (refs 5, 6) in rhombomere 4 (r4). Here we report that absence of Hoxb-1 leads to changes in r4 identity. In mutant mouse embryos, molecular markers indicate that patterning of r4 is initiated properly but not maintained. Cellular analysis by DiI tracing reveals that the r4-specific facial branchiomotor (FBM) and contralateral vestibuloacoustic efferent (CVA) neurons are incorrectly specified. In wild-type mice CVA neurons migrate from r4 into the contralateral side, and we found in lineage analysis that FBM neurons migrate from r4 into r5. In mutants, motor neurons differentiate but the CVA and FBM neurons fail to migrate into their proper positions. Instead, they form a motor nucleus which migrates atypically, and there is a subsequent loss of the facial motor nerve. These results demonstrate that, as a part of its role in maintaining rhombomere identity, Hoxb-1 is involved in controlling migratory properties of motor neurons in the hindbrain.