Background This study examines obesity and factors associated with obesity in children aged 11–13 years in the UK. Methods 1147 children from ten secondary schools participated in a health survey that included blood samples, fitness test and anthropometric measures. Factors associated with obesity were examined using multilevel logistic regression. Findings Of the children examined (490 male; 657 female) a third were overweight, 1 in 6 had elevated blood pressure, more than 1 in 10 had high cholesterol, 58% consumed more fat than recommended, whilst 37% were classified as unfit. Children in deprived areas had a higher proportion of risk factors; for example, they had higher blood pressure (20% (deprived) compared to 11% (non-deprived), difference: 9.0% (95%CI: 4.7%–13.4%)). Obesity is associated with risk factors for heart disease and diabetes. Maintaining fitness is associated with a reduction in the risk factors for heart disease (high blood pressure and cholesterol) but not on risk factors for diabetes (insulin levels). In order of importance, the main risk factors for childhood obesity are being unfit, having an obese father, and being large at birth. Conclusion The high proportion of children with risk factors suggests future interventions need to focus on community and policy change to shift the population norm rather than targeting the behaviour of high risk individuals. Interventions need to focus on mothers’ lifestyle in pregnancy, fathers’ health, as well as promoting fitness among children. Obesity was not associated with deprivation. Therefore, strategies should be adopted in both deprived and non deprived areas.