The Drosophila sine oculis (so) gene is a high hierarchy and essential gene in the developmental pathway of the fly visual system. so is the founder member of the SIX family, which in the fly also includes the genes D-six3 (optix) and D-six4 and in vertebrates, the SIX1, SIX2, SIX3, SIX4, SIX5 and SIX6 genes. In addition to a homeobox domain, all members of the SIX family of proteins contain a characteristic highly conserved region denoted as the SIX domain. Genes of the SIX family encode nuclear homeobox proteins that have been proposed to be the DNA binding domain of a transcription complex that also includes members of the EYA (eyes absent) gene family. A number of studies suggest important roles for the SIX genes in the development of the anterior part of the vertebrate CNS and eye, in myogenesis and perhaps also in the development of the auditory system, kidneys, digits and connective tissue. This review presents a comprehensive description of the current knowledge of the human SIX gene family, including unpublished data from our laboratories. We describe the genomic organization and structure of the human SIX genes and discuss their phylogenetic relationships in the context of the evolution of the SIX gene family. Using data mostly available from other species we discuss the developmental expression patterns and function of the SIX genes. Lastly, we present the current knowledge of the involvement of the SIX genes in human disease.