Most of the complications of juvenile obesity are due to metabolic disturbances induced by an excessive accumulation of fat which leads to chronic diseases like type 2 diabetes mellitus (T2DM) and cardiovascular disease (CVD). Finding effective ways of identifying obese paediatric patients who are at increased risk of developing cardiovascular and metabolic complications has been recognised to be a promising strategy to improve prevention of complications of early obesity. Moreover, correctly identifying obese children who are already affected by metabolic co-morbidities should be a clinical priority. According to the state of the art summarised in this review, traditional metabolic variables included in the definitions of metabolic syndrome (MS), pre-diabetes, non-alcoholic fatty liver disease (NAFLD)/non-alcoholic steato-hepatitis and, in obese girls, the presence of polycystic ovary syndrome are the best available longitudinal predictors of CVD and T2DM among obese children and adolescents. In clinical practice, traditional metabolic variables included in the definitions of MS should be assessed in all obese children and adolescents; fasting metabolic variables have been proposed to identify obese patients likely to be affected by impaired glucose tolerance or T2DM, and ultrasound has proved to be a valid surrogate for biopsy in the diagnosis of NAFLD. Further large longitudinal and cross-sectional studies are needed to improve our chances of identifying obese youth at the highest metabolic risk.