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Background Metabolic syndrome (MetS) is defined as a cluster of risk factors for predicting type 2 diabetes mellitus and cardiovascular disease. Objectives This cross-sectional study aimed to develop a cut-off value for fat versus lean mass ratio (FLMR) in predicting MetS and to investigate the association between this indicator with MetS and its components. Methods Subjects comprised 238 Malay adolescents (79% female) aged 18–19 years old. Anthropometric assessment comprised weight, height and waist circumference (WC). Body composition was measured using bioelectrical impedance analysis techniques while blood pressure was measured using a blood pressure monitor. Fasting blood glucose, total cholesterol , triglycerides, high-density lipoprotein cholesterol (HDL-c), and low-density lipoprotein cholesterol were determined from an overnight fasting blood sample. MetS was determined based on International Diabetes Federation (2007) definition for adolescents aged 16-year-old and above. Results The prevalence of MetS was 2.1%. Receiver Operating Characteristics curve analysis revealed that the optimal cut-off value for FLMR was 0.441 with an Area Under the Curve of 0.874 (95% CI: 0.825, 0.913); with sensitivity of 80.0% and specificity of 71.0%. FLMR cut-off of 0.441 was associated with high WC ( p < .001), low HDL-c ( p < .001) and MetS ( p < .05). Binary Logistic Regression analysis revealed that adolescents with high WC, low HDL-c and MetS had higher odds of developing increased FLMR than the cut-off value with an odds ratio (OR) of 43.4 (95% CI: 9.7,193.9), 4.7 (95% CI: 2.3,9.8) and 13.3 (95% CI: 1.5,121.2), respectively. Conclusion FLMR possesses fair discriminatory ability in identifying MetS among adolescents and significant association exists between FLMR and MetS and some of its components.