To evaluate the association between severe hypomagnesemia and the low-grade inflammatory response in subjects with metabolic syndrome (MetS), ninety-eight individuals with new diagnosis of MetS were enrolled in a cross-sectional study. Pregnancy, smoking, alcohol intake, renal damage, hepatic disorders, infectious or chronic inflammatory diseases, malignancy, use of diuretics, statins, calcium antagonist, antioxidants, vitamins, anti-inflammatory drugs, or previous oral magnesium supplementation were exclusion criteria. According serum magnesium levels, participants were assigned to the following groups: 1) severe hypomagnesemia (≤1.2 mg/dL); 2) hypomagnesemia (>1.2≤1.8 mg/dL); 3) Normal serum magnesium levels (>1.8 mg/dL). The low-grade inflammatory response was defined by elevation of serum levels of (hsCRP >1.0 ≤10.0 mg/L) or TNF-alpha (TNF-α ≥3.5 pg/mL). Severe hypomagnesemia, hypomagnesemia, and normomagnesemia were identified in 21 (21.4%), 38 (38.8%), and 39 (39.8%) individuals. The ORs, adjusted by WC, showed that severe hypomagnesemia (OR: 8.1; CI 95%: 3.6-19.4 and OR: 3.7; CI 95%: 1.1-12.1), but not hypomagnesemia (OR: 1.8; CI 95%: 0.9-15.5 and OR: 1.6; CI 95%: 0.7-3.6), was strongly associated with elevated hsCRP and TNF-α levels, and that normomagnesemia exhibited a protective role (OR: 0.32; CI 95%: 0.1-0.7 and OR: 0.28; CI 95%: 0.1-0.6) for elevation of CRP and TNF-α. Results of this study show that, in subjects with MetS, severe hypomagnesemia, but not hypomagnesemia, is associated with elevated concentrations of CRP and TNF-α.