In this study we have cloned the chick Hoxa-2 gene and analysed its expression during early development. We find that Hoxa-2 has a rostral limit of expression in the rhombencephalic neural tube corresponding precisely to the boundary between rhombomeres (r)1 and 2; a limit further rostral than any other Hox gene reported to date. Neural crest migrates from r2 to populate the first branchial arch, yet although Hoxa-2 is expressed down the full dorsoventral extent of r2 during the phase of neural crest emigration, there is no Hoxa-2 expression in either the emergent neural crest or in the first branchial arch. Conversely, at the level of r4, both the neural tube and the neural crest cells, which migrate out of this rhombomere to populate the second branchial arch, express Hoxa-2. Other Hox genes expressed in the rhombencephalic neural tube demonstrate a transfer of expression from neural tube to neural crest at all axial levels of expression. Hoxa-2 is thus unusual in demonstrating separate anterior expression limits in neural tube and neural crest; this allowed us to test whether Hox gene expression patterns in neural crest are determined by migratory pathways or are prespecified by the site of origin in the neuroepithelium. Grafting experiments in which pairs of rhombomeres were transplanted to ectopic sites at the time of rhombomere boundary formation reveal a prepatterning of the neural crest with respect to Hoxa-2 expression. The decision to down-regulate Hoxa-2 expression in r2-derived neural crest, but to maintain Hoxa-2 expression in r4-derived neural crest is intrinsic to the premigratory crest cell population. Thus, following grafting of r4 to the r2 site and vice-versa, Hoxa-2 expression is maintained in r4-derived neural crest, but lost in r2-derived neural crest.