Urine has become one of the most attractive biofluids in clinical proteomics as it can be obtained non-invasively, in large quantities and is stable compared to other biofluids. The urinary proteome has been studied by almost any proteomic technology, but mass-spectrometry-based urinary protein and peptide profiling has emerged as most suitable for clinical application. After a period of descriptive urinary proteomics the field is moving out of the discovery phase into an era of validation of urinary biomarkers in larger prospective studies. Although, mainly due to the site of production of urine, the majority of these studies apply to the kidney and the urinary tract, recent data shows that analysis of the urinary proteome can also be highly informative on non urogenital diseases and be used in their classification. Despite this progress in urinary biomarker discovery, the contribution of urinary proteomics to the understanding of the pathophysiology of disease upon analysis of the urinary proteome is still modest, mainly due to problems associated to sequence identification of the biomarkers. Until now, research has focused on the highly abundant urinary proteins and peptides but analysis of the less abundant, and naturally existing urinary proteins and peptides still remains a challenge. In conclusion, urine has evolved as one of the most attractive bodyfluids in clinical proteomics with, potentially, a rapid application in the clinic.