Urinary proteomics is emerging as a powerful non-invasive tool for diagnosis and monitoring of variety of human diseases. We tested whether signatures of urinary polypeptides can contribute to the existing biomarkers for coronary artery disease (CAD). We examined a total of 359 urine samples from 88 patients with severe CAD and 282 controls. Spot urine was analyzed using capillary electrophoresis online coupled to electrospray ionization- time of flight mass spectrometry (CE-ESI-TOF-MS) enabling characterization of more than 1000 polypeptides per sample. In a first step a “training set” for biomarker definition was created. Multiple biomarker patterns clearly distinguished healthy controls from CAD patients and we extracted 15 peptides that define a characteristic CAD signature panel. In a second step, the ability of the CAD specific panel to predict presence of CAD was evaluated in a blinded study using a “test set”. The signature panel showed sensitivity of 98% [95% CI 88.7 to 99.6] and 83% specificity [95% CI 51.6 to 97.4]. Further, the peptide pattern significantly changed towards the healthy signature correlating with the level of physical activity after therapeutic intervention. Our results show that urinary proteomics can identify CAD patients with high confidence, and might also play a role in monitoring the effects of therapeutic interventions. The workflow is amenable to clinical routine testing suggesting that non-invasive proteomic analysis can become a valuable addition to other biomarkers used in cardiovascular risk assessment.