Objective: Metabolic syndrome has high prevalence in patients with Schizophrenia in comparison with normal population. According to high prevalence of metabolic syndrome in subject with higher than 40 years, so the aim of this study was to comparison of metabolic syndrome in patients with Schizophrenia treated with atypical antipsychotics and control group. Methods: This cross-sectional study was done in 100 patients with Schizophrenia treated with atypical antipsychotics and 135 healthy subjects. The prevalence of metabolic syndrome and individual metabolic syndrome factors were evaluated in less and more than 40 years. Results: In patients less than 40 years, the prevalence of metabolic syndrome was 18.6 in patients with Schizophrenia treated with atypical antipsychotics and 7 in healthy subjects. In patients more than 40 years, the prevalence of metabolic syndrome was 10 in patients with Schizophrenia treated with atypical antipsychotics and 32.8 in healthy subjects. The prevalence of metabolic syndrome in patients with schizophrenia was 3 times (OR = 3, CI95: 1.01-8.9) more than control group in patients less than 40 years, and 0.2-fold (OR=0.2, CI95: 0.06-0.83) in patients with more than 40 years. Conclusion: Metabolic syndrome had high prevalence in schizophrenia patient with less than 40 years old, however patients with schizophrenia had been screened for metabolic syndrome in younger age and this concern in patients with older than 40 years had minor importance