We developed a proteomics-based technology for the non-invasive detection of urothelial and prostate carcinoma. Using capillary electrophoresis coupled to mass spectrometry, disease-specific changes in the urinary proteome were detected and subsequently relevant polypeptides were employed as disease-specific biomarkers. Here we report the results of various studies including approximately 1,000 patients with different diseases and healthy volunteers. The results of these studies revealed that prostate and urothelial carcinoma can be detected by using disease-specific polypeptide patterns. Preliminary results also indicate that the tumour stage of an urothelial carcinoma can be estimated by this approach. In conclusion, this new and non-invasive application might help to improve the diagnostic methods already available.