Previously, we identified FAM3C as a candidate gene for autosomal recessive nonsyndromic hearing loss locus 17 (DFNB17). This gene has since been found to be a member of a cytokine-like gene family, but its function has not been determined. The purpose of this study was thus to elucidate the gene structure and pattern of expression, providing information that might allow a hypothesis to be developed about FAM3C function of in the inner ear. To do this we analyzed its mouse ortholog, Fam3c. Fam3c was found to be ubiquitously expressed in all analyzed tissues, and had two major transcript variants presumed to result from an alternative use of two distinct polyadenylation signals. In situ hybridization experiments revealed a predominant Fam3c pattern of expression in the nonsensory epithelium of the growing semicircular canals at embryonic day (E) 15.5. This expression pattern resembles the known pattern of the Nkx5 homeobox genes. Analysis of the Fam3c promoter region demonstrated a putative Nkx5.1 binding site. Based on our findings, we hypothesize that Fam3c may be a downstream target gene for the Nkx5.1 transcription factor, and may thus be involved in cell differentiation and proliferation during inner ear embryogenesis. Additionally, analyses of putative amino acid sequences of FAM3C orthologous proteins showed that their primary and secondary structures and overall topology were highly conserved. Further study is underway to determine the role of FAM3C in inner ear development.