The paediatric obesity epidemic is well documented. Recently, there has also been the emergence of type 2 diabetes and the metabolic syndrome (MetS) among children and adolescents. Although it is well known that obesity is linked to the metabolic syndrome in youth, the role of physical activity and fitness on the metabolic syndrome is unclear. The purpose of this review was to examine the concepts of and associations between fitness, fatness and the MetS in children and adolescents. In general, the association between fatness and the MetS (or components of the MetS) is stronger than those for fitness. Furthermore, the correlation between fatness and the MetS remains significant after controlling for fitness, whereas the correlation between fitness and MetS does not remain significant after controlling for fatness. When subjects are cross-tabulated into categories (fat-fit, etc.), there is good evidence that fitness attenuates the MetS score among fat children and adolescents. The reasons for these observations possibly involve genetics, adipocytokines and mitochondrial function. Further study is needed to understand the role of physical activity and other environmental factors on this phenomena. In addition, longitudinal studies of the fat-fit phenotype are required and should include measurements of the hormonal mileau, adipokines and the oxidative capacity of skeletal muscle during childhood and adolescence.