Until recently, there has been no unified definition of the metabolic syndrome (MetS) in the youth. Therefore, the prevalence of MetS and its association with potential correlates are largely unknown. The objective was to quantify the prevalence, identify the correlates, and examine the independent associations between potential correlates with MetS. A population-based cohort study was conducted in 10- and 15-y-old youth from Estonia, Denmark, and Portugal (n = 3193). MetS was defined according to the International Diabetes Federation. Correlates included maternal socioeconomic status, body mass index (BMI), hypertension, and prevalent diabetes and maternally reported child’s birth weight and duration of breastfeeding. Data on sexual maturity, objectively measured physical activity, cardiorespiratory fitness, self-reported sports participation, television viewing, and regular play were collected for the children. The prevalence of MetS was 0.2% and 1.4% in 10- and 15-y-olds, respectively. Cardiorespiratory fitness (standardized odds ratio: 0.33; 95% CI: 0.15, 0.75), physical activity (standardized odds ratio: 0.40; 95% CI: 0.18, 0.88), and maternal BMI (standardized odds ratio: 1.61; 95% CI: 1.11, 2.34) were all independently associated with MetS after adjustment for sex, age group, study location, birth weight, and sexual maturity. An increase in daily moderate-intensity physical activity by 10–20% was associated with a 33% lower risk of being categorized with MetS. High maternal BMI and low levels of cardiorespiratory fitness and physical activity independently contribute to the MetS and may be targets for future interventions. Relatively small increases in physical activity may significantly reduce the risk of MetS in healthy children.