The adult mammalian kidney is generated by the differentiation and integration of several distinct cell types, including the nephrogenic mesenchyme, ureteric epithelium, stromal and endothelial cells. How and where these cell types are generated and what signals lead to their differentiation and integration into a functional organ system is a main focus of current studies. Herein, we review the formation of distinct cell types within the adult mammalian kidney; what is understood regarding their origin and the signaling pathways that lead to their formation and integration; morphogenetic changes the metanephric kidney undergoes during development; and what is known regarding the role of Hox genes in these processes.