The objective of this paper was an evaluation of change in prevalence of overweight and obesity in Czech children, and a comparison of cut-off points for body mass index references from the Czech Republic (CzR), International Obesity Task Force and WHO. The authors conducted a survey in 7-year-old children, and compared data from 1951, 1981, 1991, 2001 and 2008 (WHO cut-offs). 2008 data were evaluated according to different cut-offs. Results showed that since 1951 in boys, overweight prevalence increased from 13.0% in 1951 to 26.8% in 2001, in girls from 10.9% to 22.9%. Obesity increased in boys from 1.7% to 8.3%, in girls from 1.7% to 6.9%. From 2001 to 2008 obesity in boys increased; obesity in girls and overweight in both genders decreased. In 2008 cohort the following values were found: overweight and obesity: CzR criteria, percentage was lowest (14.8% boys and 11.1% girls); WHO criteria, highest prevalence (23.5% boys and 19.5% girls); obesity: lowest ratio International Obesity Task Force criteria (4.4% boys, 3.3% girls), highest ratio boys WHO criteria (10.0%), girls CzR criteria (5.0%). Overweight and obesity prevalence increased in 7-year-old Czech children since 1951; since 2001 prevalence is plateauing with exception of boys. Using different body mass index references resulted in marked differences in overweight and obesity prevalence.