During recent years, the proteomics field has moved onward to clinical applications, particularly for biomarker discovery, diagnostics and prognostics of human diseases. The urine is one of the ideal clinical samples for such applications because it is readily available in almost all patients, and its collection is very simple and non-invasive. Urinary proteomics thus becomes one of the most interesting subdisciplines in the clinical proteomics area. This article highlights and updates recent progress in the urinary proteomics field for clinical applications.