Of the nine known PAX genes, only two (PAX2 and PAX8) are expressed in the developing kidney. Genetic evidence in mice and humans indicates that PAX2 plays a critical role in normal renal development and may sit atop a molecular cascade which unfolds during the transition from undifferentiated mesenchyme to the early stages of nephrogenesis. Less is known about the role of PAX8 in kidney development; although PAX8 is expressed in the S-shaped body and early proximal tubule, preliminary data suggest that renal morphogenesis is unaffected by its absence. In this review, we discuss the basic aspects of PAX gene structure and function and how mutations of PAX2 might interfere with structure of the developing nephron.