Objectives. To report 5-year changes in the prevalence of overweight and obesity in 11-year-old children in Cyprus. Methods. This was a school-based study performed in Cyprus. A total of 14 090 11-year-old children (males: 51.2%), who had been examined in the 1997-8 and 2002-3 school years, were included in the study. The International Obesity Task Force (IOTF) cut-offs were used to define overweight and obese subjects, and logistic regression models were used to estimate 5-year trends. Results. The overall prevalence of overweight children was slightly higher in the second period but this change was not statistically significant. There was only a significant increase in overweight boys in rural areas; odds ratio (OR) (95% confidence interval [CI]) for the 5-year period was 1.33 (1.10, 1.62; p = 0.004). The overall relative increase in obesity was 17.9% and the OR (95% CI) was 1.22 (1.07, 1.38; p = 0.003). Although the prevalence of obesity was higher in males in both periods, the relative increase was substantially higher in females, 29.6% vs. 11.4%. The relative increase was also higher in rural (35.9%) compared with urban areas (8.7%); ORs (95% CI) 1.46 (1.17, 1.81) vs. 1.10 (0.94, 1.29), respectively. Conclusions. This is the first report documenting increasing rates of obesity among school-aged children in Cyprus. Females and children living in rural areas experienced the most striking increases. The prevalence of overweight increased only in males living in rural areas.