Congenital urinary tract obstruction (diagnosed antenatally by ultrasound screening) is one of the main causes of end-stage kidney disease in children. The extent of kidney injury in early gestation and the resultant abnormality in kidney development determine fetal outcome and postnatal renal function. Unfortunately, the current approach to diagnostic evaluation of the severity of injury has inherently poor diagnostic and prognostic value because it is based on the assessment of fetal tubular function from fetal urine samples rather than on estimates of the dysplastic changes in the injured developing kidney. To improve the outcome in children with congenital urinary tract obstruction, new biomarkers reflecting these structural changes are needed. Genomic and proteomic techniques that have emerged in the past decade can help identify the key genes and proteins from biological fluids, including amniotic fluid, that might reflect the extent of injury to the developing kidney.