The main focus of urinary proteome analysis in nephrology is currently on detection and identification of polypeptides that significantly alter (in abundance, distribution, etc.) during (patho)physiological changes of the kidney structure and/or function. Capillary electrophoresis coupled online to electrospray ionization time-of-flight mass spectrometry (CE-MS) was applied to human urine to identify biomarkers for clinical diagnostics. To extract the information of the CE-MS spectra in a timely fashion, software was designed to automatically deconvolute and normalize the spectra. Furthermore, bioinformatics and statistic approaches were used to discriminate patients with different diseases and healthy individuals, respectively. Samples from patients with renal diseases display polypeptide patterns that differ significantly from those obtained from healthy individuals. Examining series of patients with the same disease allowed the establishment of polypeptide patterns typical for specific diseases. This permits the search for the disease-specific peptide markers. The combinations of several polypeptides found in urine are forming a specific pattern, which is indicative not only for the particular disease, but also for the stage of disease. These results show that proteome analysis with CE-MS of urinary polypeptides in patients with different renal diseases and urological disorders can display the current status of the kidney or the urogenital tract. This advancement offers the early diagnosis of different nephrological diseases.