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The type of fat consumed in the Mexican diet could predispose to the development of Metabolic Syndrome (MS) which has been associated with an increased risk to develop cardiovascular disease and type 2 diabetes mellitus. Our study included adolescents between 12 and 16 years of age, divided in two groups: Control Group (n = 31) and MS Group (n = 44). Waist circumference, blood pressure, fasting glucose, triglycerides, and HDL-cholesterol were determined. Erythrocytes’ fatty acids methyl esthers were quantified using gas chromatography with ionized flame detector. We identified 16 fatty acids (FA) with chain lengths from C12 to C24, with emphasis in four trans FA (TFA) isomers: vaccenic (C18:1n7t), elaidic (C18:1n9t), linoelaidic (C18:2n6t), and conjugated linoelaidic acids (C18:2n7t). MS Group had a less proportion of: myristic (C14), palmitoleic (C16:1), C18:1n7t, and linoleic acids (C18:2); and a higher one of C18:1n9t, C18:2n7t, and nervonic acids (C24:1) when compared to the control group. C24:1 and C18:1n9t had a significant positive association with MS (OR = 14.17 and OR = 12.94, respectively); whereas C14 (OR = 0.14), C18:1n7t (OR = 0.14), and C18:2 (OR = 0.22) appear to have a protective effect against the disease. The proportion of specific FAs in erythrocytes’ membranes differs between adolescents with MS and healthy controls; these FA not only showed a strong association with MS, but also correlated with most of its individual components. Interestingly, TFA displayed an antagonic behavior; while C18:1n9t had a strong association with MS, apparently C18:1n7t confers a protective effect; these results suggest that analyzing each TFA separately will constitute a more accurate approach to determine the role of TFAs in the pathogenesis of MS or other related metabolic disorders.