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Knowledge about variations in the health status of patients seeking primary care in different parts of the United States is limited.To examine regional variations in the physical and mental health of patients receiving primary care in the largest integrated health care system in the United States which is operated by the Department of Veteran Affairs (VA).We performed a mailed, cross sectional survey of 54,844 patients who were enrolled in seven VA General Internal Medicine clinics.Among the 30,690 patients who returned an initial set of screening questionnaires, the prevalence of common chronic conditions varied by as much as 60% among the seven clinics. Moreover, patients’ general health (measured by the SF-36) also varied significantly in a pattern that mirrored the observed differences in the prevalence of chronic conditions. After adjustment for important comorbid illnesses and sociodemographic factors, geographic site accounted for a small percentage of the explained variance in patient assessed health status.The substantial differences in the health of patients enrolled in different VA primary clinics have important implications for the evaluation of clinical performance and health outcomes. Most of these differences can be attributed to sociodemographic and comorbid factors.