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To assess 5-year mental disorder recognition rates and determine the natural history of mental disorders in primary care.A prospective cohort of adults presenting to a primary care walk-in clinic with a physical symptom were evaluated at baseline (n = 500) and at 5 years (n = 387) for mental disorders with the Primary Care Evaluation of Mental Disorders (PRIME-MD). Additional measures included functional status (Medical Outcomes Study SF-6; MOS-SF6), Patient Health Questionnaire-15, Satisfaction (Rand-9), unmet expectations, and symptom outcome. Patients self-reported whether their disorder was diagnosed or treated at the 5-year follow-up.At baseline, 29% of patients had a mental disorder (major depression: 8.4%, minor depression 10.4%, Panic disorder 1.4%, generalized anxiety disorder 2%, anxiety not otherwise specified (NOS) 11.4%); of these patients, 26% had more than one mental disorder. Over 5 years, 33% were recognized. Threshold disorders were more likely to be recognized (major depression 56%, panic 100%, generalized anxiety disorder 88%) than subthreshold disorders (minor depression 20%, anxiety NOS 25%). Correlates of recognition included having a threshold or multiple disorders; recognition was associated with greater likelihood of persistence. Most patients with subthreshold disorders at baseline had no disorder at 5 years and few progressed to threshold disorders (minor to major depression 12%, anxiety NOS to generalized anxiety or panic 8%).Mental disorders are common and their recognition and treatment remain low. Subthreshold disorders have a better prognosis. Patients with threshold or multiple disorders, worse functioning or persistence of their disorder were more likely to be diagnosed.