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 less than 0.001) and from 8.1% to 12.4% (P less than 0.001) for boys. In rural areas, obesity increased from 7% in 1997 to 13% in 2008 for girls (P less than 0.001), and from 8.2% to 14.1% (P less than 0.001) 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 [plus or minus] 1.9 stages in 1997 to 3.02 plus or minus 2.1 stages in 2007 for boys (P less than 0.001), and from 2.97 plus or minus 1.5 stages to 2.53 plus or minus 1.7 stages (P less than 0.001) 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.