Objective: To assess the quality of care provided in primary military clinics. Methods: A standardized assessment tool was used, with medical record audits and tracers (minimal clinical criteria for proper care of common conditions), peer-review observations of medical encounters, assessments of organization and administration, and patient satisfaction and physicians' occupational stress questionnaires. Results: Forty-three clinics and 113 physicians were assessed. Tracers were high for management of upper respiratory infections and low for low back pains and mental problems. The average encounter time was 9 minutes, and 25% of medical encounters resulted in referrals to specialists. Regular physicians performed better than reservists. Surgeons performed worst as primary health care providers. Female physicians did better than male physicians. The integration of new immigrant physicians was successful, and they expressed less occupational stress. Smaller clinics were better, with longer encounter times and better patient satisfaction scores. Conclusions: Quality assessment of primary health care is feasible in the military system, providing useful information for future improvement.