Even though there is a severe obesity problem in Cyprus, information about the contribution of predisposing lifestyle factors is limited. Our aim was to investigate the relationship between physical activity (PA), sedentary behaviour and various obesity indices [i.e. body mass index (BMI), waist circumference (WC), percentage of body fat (BF%) and 'total & abdominal obesity' (TAO)]. A national cross-sectional study of 1140 children (mean age = 10.7 +/- 0.98 years) selected by multistage sampling in Cyprus was conducted during 2004-05. Children completed a 32-item, semi-quantitative PA questionnaire, which assessed organized and free-time PA and sedentary behaviours. Weight, height and WC were collected from a random sub-sample of 622 children and obesity was defined by IOTF criteria. Body fat percentage was calculated, and TAO status was computed based on obesity status and WC [i.e. (i) both BMI/WC, (ii) either BMI/WC abnormal and (iii) both BMI/WC abnormal]. Linear and logistic regression analyses with obesity indices as dependent variables were applied after adjusting for several potential confounders. Only variables describing sedentary behaviours were retained in the final regression models in both boys and girls. Girls who spent >or=4 h/day on TV and DVD watching were almost three times more likely to be overweight or obese [OR = 2.84 (95% CI 1.08-7.47)], three times more likely to have WC >or=75th percentile [OR = 3.25 (95% CI 1.06-9.98)] and 3.5 times more likely to have >or=30% body fat [OR = 3.63 (95% CI 1.01-12.98)], while in boys, even though the same variable was retained in almost all final models, it did not reach statistical significance. Sedentary behaviours such as TV watching may be more important predictors of children's various obesity indices than PA behaviours. Interventions targeting sedentary behaviours, such as TV watching, may help in the prevention and treatment of obesity among Cypriot children.