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Background: This study aimed to establish a comprehensive screening and referral system for chronic non-communicable diseases (CNCD) in the routine primary health care, and to determine the prevalence of diabetes, pre-diabetes, metabolic syndrome, and dyslipidemia in adult population invited by public announcement to the Health clinics in Isfahan, Iran. Methods: This survey was conducted from March 2010, and the current paper presents data obtained until November 2011. To provide health services for prevention and control of CNCDs, with priority of type2 diabetes mellitus, Health clinics were established in different parts of Isfahan city with a population of approximately 2,100,000 in Iran. The general populations aged 30 years and above were invited to the Health clinics by public announcement. Results: A total of 198972 participants were screened. The mean age of participants was 47.8 years (48.5 men, 47.3 women), with a range of 1 to 95 years old and standard deviation of 12.3 years (12.7 men, 12.1 women). Overall, 22% of participants had impaired fasting glucose, 25% had hypercholesterolemia, 31% had hypertriglyceridemia, and 20% had metabolic syndrome. Conclusion: The high prevalence of dysglycemia and diabetes in our survey may serve as confirmatory evidence about the importance of mass screening and early diagnosis of CNCDs′ risk factors. Our model of establishing Health clinics, as a comprehensive referral system in the routine primary health care can be adopted by Middle Eastern countries, where CNCDs notably diabetes are an emerging health problem.