Homeodomain-containing transcription factors are essential for a variety of processes in vertebrate development, including organogenesis. They have been shown to regulate cell proliferation, pattern segmental identity and determine cell fate decisions during embryogenesis. During nephrogenesis, homeobox genes play an important role at multiple developmental stages, from the early events in intermediate mesoderm to terminal differentiation of glomerular and tubular epithelia. Increasingly sophisticated genetic approaches will probably reveal additional functions for this class of transcription factors in the developing kidney and lead to the identification of critical downstream target genes.