New disease-specific biomarkers are sorely needed within all fields of medicine. This review covers the current literature of biomarkers within pediatric urology and discusses future perspectives and directions for biomarker discovery.Biomarkers can be used to diagnose disease, monitor response, or sub-classify disease. Within pediatric urology, numerous markers for renal obstruction [ureteropelvic junction (UPJ)] and vesicoureteral reflux (VUR) have been identified and have shown initial promise; however, no markers have been rigorously validated or demonstrated to be clinically effective. Recent advances in proteomic technologies may provide a new discovery method to identify panels of markers for specific disease.New clinically significant biomarkers of UPJ or VUR that can improve the diagnostic capability or help determine risk for renal damage are sorely needed. However, rigorous clinical validation of previously identified markers has been limited. Other studies have demonstrated that combining various markers may help improve the ability to define clinical relevance. To improve biomarker discovery efforts, a combination of focused biomarker studies, potentially using new advanced proteomic technologies, and well designed clinical studies are needed.