Glutaric acidemia type II and carnitine palmitoyltransferase type II deficiency are rare, but potentially treatable, inherited metabolic diseases. Hallmarks of the early onset form of both conditions are renal abnormalities and neonatal metabolic crisis. In this article, we report on two newborns with cystic renal dysplasia as a leading sign of these metabolic diseases. We focus on the clinical presentation and discuss the diagnostic tests and the available therapeutic options. We conclude that prenatal diagnosis of cystic renal dysplasia should alert the physician to the possibility of these metabolic diseases. This knowledge should prompt careful observation and, where necessary, early intervention during the postnatal period of catabolism.