OBJECTIVE: This study aimed to estimate the prevalence of overweight and obesity and investigate associated factors in a representative sample of Cretan school children. METHODS: As part of a cross-sectional study in children aged 10-12 years (n = 481, 48% boys) in 27 (urban and rural) schools in Crete, Greece, the rates of overweight and obesity were estimated and multiple logistic regression was used to explore the relationship between several factors and body mass index (BMI). RESULTS: It was shown that 28% and 13% of children were overweight and obese, respectively. Factors affecting children's BMI classification included: gender (95% CI: 0.21 to 0.56); birth weight (95% CI: 1.33 to 3.46); parental overweight or obesity (95% CI: 1.11 to 6.5 and 95% CI: 4.37 to 30.7 for one and both overweight or obese parents, respectively), paternal educational level (95% CI: 0.89 to 3.48 and 95% CI: 1.49 to 6.13 for low and high educational level, respectively); and cardiovascular fitness levels (95% CI: 0.87 to 0.92). CONCLUSION: The combined prevalence of overweight and obesity was alarmingly high in the current population (41%); several physiological, behavioural and social factors were shown to affect children's BMI status. These findings highlight the extent of the child obesity problem in Crete and support the need for actions to be taken at a national level to tackle the obesity epidemic.