PURPOSE: To compare 12-year (1997-2008) trends in the distribution of Body Mass Index (BMI) status and physical fitness test performances among 8- to 9-year-old Greek children living in rural and urban areas. METHODS: Population data derived from 11 national school-based health surveys conducted from 1997 to 2008. Anthropometric measurements and physical fitness test performances (ie, multistage shuttle run, vertical jump, small ball throw, and 30-meter sprint) from 725,163 children were analyzed. Distribution between rural and urban areas was based on the Hellenic National Statistics Service (HNSS) criteria. FINDINGS: Trend analysis showed an increase in the prevalence of obesity in children living in urban areas from 7.2% in 1997 to 11.3% in 2008 for girls (P < .001) and from 8.1% to 12.4% (P < .001) for boys. In rural areas, obesity increased from 7% in 1997 to 13% in 2008 for girls (P < .001), and from 8.2% to 14.1% (P < .001) for boys. The annual rate of obesity increase was 40%-50% higher in children from rural areas. Nevertheless, rural children presented better performances in all of the physical fitness tests examined. Specifically, mean values of aerobic performance decreased from 3.58 ± 1.9 stages in 1997 to 3.02 ± 2.1 stages in 2007 for boys (P < .001), and from 2.97 ± 1.5 stages to 2.53 ± 1.7 stages (P < .001) for girls in urban areas, whereas in rural areas, the correspondent values were not significantly different between 1997 and 2007. CONCLUSIONS: Childhood obesity rates are higher in rural compared with urban areas in Greece, despite an apparent higher fitness level of children living in rural areas.