Homeodomain-containing transcription factors have crucial functions in most aspects of cellular function and embryonic development in both animals and plants. Hmx proteins are a sub-family of NK homeodomain proteins and previous research has shown that they have crucial functions in the development of sensory structures such as the eye and the ear. However, the functions of Hmx proteins in spinal cord development have not been analyzed.Here we show that zebrafish hmx2 and hmx3a are co-expressed in spinal dI2 and V1 neurons, whereas hmx3b, hmx1 and hmx4 are not expressed in the spinal cord. Using mutational analyses, we demonstrate that, in addition to its previously demonstrated role in ear development, Hmx3a is required for survival to adulthood, lateral line progression and correct specification of spinal interneuron neurotransmitter fates. However, despite the fact that hmx2 and hmx3a have similar expression patterns during embryonic development, we have not detected any requirement for Hmx2 in these developmental processes, even when almost all of the hmx2 locus is deleted. We have also not detected any redundancy between hmx2 and hmx3a: double mutants have identical phenotypes to hmx3a single mutants. Even more surprisingly, we have found that Hmx3a does not require its homeodomain for its roles in viability or embryonic development. This is, to our knowledge, the first time that such a prototypical homeodomain protein has been shown not to require its homeodomain.Hmx2 in viability, or otolith, lateral line or specification of spinal interneuron neurotransmitter fates, even when almost all of the hmx2 locus is deleted (in our most severe mutant allele, hmx2 SU39 , only 84 nucleotides of 5' sequence and 57 nucleotides of 3' coding sequence remain). We have also not detected any redundancy between hmx2 and hmx3a: hmx2;hmx3a double mutants have identical phenotypes to severe hmx3a single mutants. Even more surprisingly, we have found that Hmx3a does not require its homeodomain for its roles in viability or embryonic development. This is, to our knowledge, the first time that such a prototypical homeodomain protein has been shown not to require its homeodomain.