We conducted a cross-sectional study of Indigenous youths residing in the Torres Strait region of Australia to assess the prevalence of obesity and the metabolic syndrome. Data on body mass index (BMI), waist circumference, blood pressure, presence of acanthosis nigricans and blood glucose were collected. Fasting glucose, insulin, C-Peptide, HbA1c and lipids were measured, and an oral glucose tolerance test was performed in those with a BMI greater than 25 (childhood-equivalent cut-points) or fasting glucometer reading >5.5 mmol/L. Of 158 youths, 31% were overweight and 15% were obese, 38% had enlarged waist circumference consistent with central obesity, 43% had acanthosis nigricans and 27% were hypertensive. More females than males had enlarged waist circumferences (59% vs. 13%, P < 0.001). Among overweight or obese youth, 56% had significantly elevated insulin (P = 0.021); they also had higher HOMA-IR (P = 0.002). The metabolic syndrome was present in 17% of all youths (mostly females) and in 33% of the overweight or obese subgroup. Type 2 diabetes was diagnosed in two youths. These very high proportions of overweight or obese Torres Strait youth with metabolic risk factors have major public health implications.