In 2007, WHO published a new reference for assessing the nutritional status of children and adolescents aged 5 to 19 years, including body mass index (BMI) by sex and age. To compare the nutritional assessment by BMI in schoolchildren and adolescents using the actual Chilean Ministry of Health norm (NCHS) and the new WHO reference 2007. Retrospective cohort study of 117,745 newborns, with nutritional assessment on first year of basic education (1997) and later in high education (2005). We analyzed the nutritional status according to BMI for age in relation to the NCHS references and WHO 2007, in standard deviations (SD) and percentiles. We analyzed the agreement between the different references with the Kappa index. There were small differences in the nutritional classification in first grade (6,4 ± 0,3 years) between the three references. Underweight prevalence was slightly higher with both WHO references, overweight with WHO in standard deviation and obesity with WHO percentiles, at first grade of high school (14,4 ± 0,3 years). The main difference was in relation to classification of obesity (≥ percentile 95), where 43,9% of obese by WHO percentiles were considered overweight with NCHS (87,3% concordance Kappa 0,75). The diagnostic concordance between the three criteria was the order of 90%. There are some differences between NCHS and WHO, and between both WHO reference, depending on the cutoff point used. The adoption of one or other reference should depend on the biological hazards associated with it.