The kidney is the most common site of congenital malformations that result in impaired renal function. Yet, the molecular mechanisms that control renal malformations are poorly understood. The Hedgehog signaling pathway plays critical roles during mammalian organogenesis. Aberrant Hedgehog signaling results in severe congenital abnormalities, including renal malformations. Here, we review the current body of knowledge on Hedgehog signaling during renal morphogenesis and highlight the gaps in our understanding. Furthermore, we propose mechanisms by which Hedgehog signaling contributes to both normal and abnormal renal development.