Background: To quantify the frequency of metabolic syndrome amongst individuals suffering from some chronic diseases and to compare them with the data obtained from healthy population. Methods: Manuscripts published on the prevalence of metabolic syndrome between 2000 and 2016 were identified through the following databases; Magiran, SID, and Iran Medex as well as PUBMED, EMBASE, MEDLINE, Web of Science, Scopus, and Google scholar using related MESH terms. Studies included if they had published quantitative estimates and measure of variability and/or confidence limits in the individual with the following diseases: diabetes, cardiovascular disease, cancer, periodontal, arthritis, polycystic ovary syndrome, Non-alcoholic fatty liver, psychiatric disorder, kidney and chronic disease. Data were analyzed with Stata, version 11. Results: A total of 62 articles selected for the final stage of this meta-analysis. The pooled prevalence of metabolic syndrome among diabetes, those with cardiovascular diseases, cases with renal failure, patients with NAFLD, periodontal subjects and individuals by arthritis were significantly higher than healthy population (P < 0.05). The risk of aforementioned diseases was found to be two to six times higher in those with metabolic syndrome than the normal population. Comparably, there was an inverse association between metabolic syndrome and mental disorders. Conclusions: Our findings suggest the early recognition, control and prevention of the metabolic syndrome and its individual components in the general population.