Development of the mammalian urogenital system requires a balance between survival and programmed cell death. Pro-survival molecules are crucial in preserving metanephric mesenchyme viability, and thus allowing nephrogenesis to proceed. At the same time, localized areas of apoptosis mediated by effector caspases are required for the appropriate morphogenesis of the kidney and urinary tract. Activation of the intrinsic pathway of apoptosis seems to be fundamental to the progression of cell death necessary to aid ureteric bud branching, nephrogenesis, and ureter-bladder connection. Here, we review what is currently known about survival and apoptosis in building functional kidneys and urinary tracts.