Due to its accessibility and availability, ease of collection, and correlation with physiology and pathology, urine is an attractive source for clinical proteomics/peptidomics in urology and nephrology. Here, we review the published findings of a reproducible, high-resolution method for peptidome analysis of naturally occurring human urinary peptides and proteins - ranging from 0.8 to 17.0 kDA - using samples from renal patients analyzed by capillary electrophoresis coupled to mass spectrometry (CE-MS). CE-MS identified children with urodynamically relevant ureteric junction obstruction, vesicoureteric reflux of grades IV and V, glomerulopathies, tubulopathies, and chronic kidney disease. Our analysis revealed that the incorporation of urinary proteome analysis in the initial evaluation of children with urinary tract abnormalities will avoid side effects of radiological imaging techniques, reduce costs, and increase the quality-adjusted life years in this patient population. CE-MS can be recommended for clinical prospective studies on the analysis of naturally occurring urinary peptides in children with urinary tract diseases.