The HOXC6 homeodomain-containing proteins act as transcription factors in the genetic control of multiple genes involved in development and cell differentiation. Two HOXC6 polypeptides are encoded by a single homeobox ('HOX') gene described as 'master gene' for the crucial role it plays in the patterning and axial morphogenesis of multiple species. Transcription of the HOXC6 gene is initiated from two promoters and generates two proteins that share the same DNA-binding domain but harbor a distinct N-terminal region. Recent studies have demonstrated that both HOXC6 products can activate or repress transcription, depending on the cellular context. Functional in vivo specificity of HOXC6 proteins may be achieved through combinatorial interactions with other members of the HOX family as well as with co-factors whose identities are largely unknown. Disruption of this 'HOX code' may lead to pathology such as developmental defects.