Background Chronic magnesium deficiency is associated with obesity, hyperglycemia, hypertension and dyslipidemia. The aim of this study was to investigate the relationship between serum and dietary magnesium levels among Iranian adults with metabolic syndrome (MetS). Methods A total of 853 participants (including 269 and 584 subjects with, or without MetS, respectively) were recruited as part of the Mashhad stroke and heart atherosclerotic disorder (MASHAD) study. Demographic data, anthropometric measurements, blood pressure, biochemical parameters and serum magnesium were determined in all participants. The first quartile of serum magnesium (<0.94 mg/dl) was considered as a low value for serum magnesium. Results In this study a low serum magnesium was found in 22.7% (n = 61) of subjects with MetS and in 22.1% (n = 129) in individuals without MetS (P-value > 0.05). Dietary magnesium insufficiency [<67% of the recommended daily allowances (RDA)] was observed in 30.3% (n = 44) of individuals with MetS and 69.7% (n = 101) of individuals without MetS (P > 0.05). There were no significant differences between serum and dietary magnesium levels among subjects with MetS and individuals without MetS (P-value > 0.05). Moreover, there was no significant difference in serum and dietary magnesium levels between individuals with or without MetS (P > 0.05). A low serum magnesium was associated with a higher fasting plasma glucose in individuals with MetS (P < 0.05). Conclusions The results showed that serum and dietary magnesium status is related to several cardiovascular risk factors including body mass index, waist circumference, total cholesterol, systolic and diastolic blood pressure. Furthermore, an inverse association was found between serum magnesium levels with diabetes mellitus.

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