OBJECTIVE: We examined secular trends in physical fitness and BMI status in 8- to 9-year-old Greek children during an 11-year period (1997-2007). METHODS: Population data derived from a yearly health survey performed in over 85% of Greek schools. Anthropometric measurements and physical fitness tests from 651,582 children were analyzed. The gender- and age-specific BMI cut-off points by the International Obesity Task Force were used to define overweight/obesity. RESULTS: Aerobic performance decreased by 4.9% (p < 0.001) for boys and 4.4% (p < 0.001) for girls between 1997 and 2007 while obesity increased by approximately 50% in both genders (p < 0.001). Time-series analyses revealed that the increasing trends in obesity were independent of the reduction in fitness levels. An increase from 21% in 1997 to 48.2% in 2007 was observed in the prevalence of the low quartile of aerobic performance for girls (p < 0.001) and from 25.7% in 1997 to 38.7% in 2007 (p < 0.001) for boys. Approximately 80% and 85% of obese boys and girls, respectively, failed to pass the low quartile of all aerobic tests in 2007. CONCLUSIONS: Inverse but independent trends in obesity and fitness levels were observed among Greek children during an 11-year period (1997-2007), a fact that predisposes our children to serious health risks as they grow older.