The aim of the study was to determine the prevalence of overweight and obesity in children in Spain using different sets of cut-off criteria, through a community-based cross-sectional study. The study was conducted in a representative sample of Spanish children between 6 and 9 years, recruited in Spanish schools, between October 2010 and May 2011. 7,569 boys and girls were selected. All were weighed and measured, and their parents were asked about their socioeconomic background, food habits and physical activity. The BMI of each was calculated, and the prevalence of overweight and obesity was determined by age and sex using Spanish reference tables (SPART), IOTF reference values, and WHO growth standards. The prevalence of overweight in boys ranged from 14.1% to 26.7%, and in girls from 13.8% to 25.7%, depending on the cut-off criteria. The prevalence of obesity in boys ranged from 11.0% to 20.9%, and in girls from 11.2% to 15.5%. The prevalence of obesity was the highest among those same children when using the SPART or WHO criteria. Overweight and obesity remain widespreading among Spanish children; a consensus on the definition of overweight and obesity cut-off criteria is necessary.