Introduction: Production of female sex hormones by the ovaries ceases gradually after natural menopause and abruptly following surgical menopause. The purpose of this study was to compare the effects of menopause on the metabolic syndrome, serum lipids, blood sugar and blood pressure. Materials and Methods: Study subjects were selected from among 5191 women, aged 20-60 years, who participated in the Tehran Lipid and Glucose Study. For our study 375 natural menopause and 71 surgical menopause were followed for 9 years. Data were collected using questionnaires. Results: Changes in metabolic and biochemical profiles of these two groups of women during follow-up were compared with each other. In this study metabolic syndrome was diagnosed in 28.7% women after natural menopause and in 32.5%, following surgical menopause. Average systolic blood pressure in the naturally menopause was higher than in surgically menopause women, adjusted for variable pre-menopausal, BMI and age, which was statistically significant. Average blood sugar in surgically menopause was higher than in naturally menopausal females, and was statistically significant. Conclusion: Compared with the naturally menopausal, women it seems that those who become menopausal following surgery have more a higher incidence of metabolic disorders, indicating that such disturbances should be considered before any surgery resulting in the loss of ovaries.