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| There is an urgent need to elucidate the mechanistic basis of chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS), as the current methods of symptom-based diagnosis and treatment have failed. Here, we propose a phenotyping system that bridges the gap between the symptom-based diagnosis and treatment of the present and the mechanistic approach of the future. Our phenotyping system uses the Chronic Prostatitis Collaborative Research Network (CPCRN)-recommended algorithm in combination with the NIH Chronic Prostatitis Symptom Index (NIH-CPSI) as a basis for diagnosis, while incorporating novel domains for quantitative assessment and stratification of CP/CPPS patients. We believe this novel system will serve to help advance our understanding of the roles of the patient's genome and proteome in the etiology of CP/CPPS. We predict that, as we begin to understand the mechanistic basis of CP/CPPS pathology and progression, we will develop specific treatments that will aim to cure the disease, rather than merely quell the symptoms.