The Hox genes encode transcription factors that are indispensable for proper spatio-temporal patterning of the vertebrate body axes. In mouse, Hoxa5 transcripts are differentially expressed in specific mesoderm-derived structures and in the most anterior domain of expression in the central nervous system (CNS). However, the functional significance of any pattern of protein-coding RNAs must be verified by correlating the presence of the protein(s) and RNAs. Here we describe the dynamic pattern of HOXA5 protein during mouse embryogenesis. The HOXA5 protein is detected as early as embryonic day (E) 9.0, and is found, as development proceeds, in several mesoderm-derived structures. In addition, the protein shows a strikingly restricted and dynamic expression pattern in the developing CNS, and is detected in both motor neurons and interneurons between E10.5-E13.5. In many mesoderm-derived tissues affected by the Hoxa5 mutation, the expression pattern of HOXA5 protein corresponds to that of the putative functional Hoxa5 transcript. However, in the CNS, this correlation is exclusively demonstrated in the most anterior domain of expression. We next focused on a complex HOXA5 expression pattern in the caudal hindbrain. In this structure, we show that HOXA5 expression is confined to the caudal region of the developing inferior olivary nucleus (ION) and dorsal lamella of the dorsal accessory olive (DAO) subnucleus. Furthermore, the ION can be transiently defined by a combinatorial expression of BRN3A and LIM1/2 transcription factors that may belong to a new dorsal neuron cell type in the caudal hindbrain defined in this study. Although HOXA5 is dispensable for the transcriptional code of ION up to embryonic day (E) 16.5, the protein expression is crucial to preserve BRN3A expression in the dorsal lamella of DAO at E18.5. To date, this is the first report for expression of any Hox5 paralog in ION. Our results suggest that HOXA5 plays a strong role in maintaining the normal transcriptional code for ION, which may affect establishment of connectivity, maturation, and synaptic stabilization of climbing fibers developed postnatally. Overall, the HOXA5 protein pattern is consistent with its proposed role in positional specification in mesodermal structures, as well as in the embryonic neuraxis.