The identification of the mammalian testis-determining factor, SRY, led to the description of a new class of genes encoding transcription factors, the SOX gene family. SOX proteins display properties of both classical transcription factors and architectural components of chromatin. The dynamic and diverse patterns of expression of SOX genes and analysis of mutations in humans, mice and Drosophila suggest that SOX factors play key roles in decisions of cell fate during diverse developmental processes.