BACKGROUND: In 2007 new World Health Organization (WHO) growth references for children aged 5-19 y were introduced to replace the National Center for Health Statistics (NCHS) references. OBJECTIVE: This study aimed to compare the prevalence of stunting, wasting, and thinness estimated by the NCHS and WHO growth references. DESIGN: NCHS and WHO height-for-age z scores were calculated with the use of cross-sectional data from 20,605 schoolchildren aged 5-17 y in 11 low-income countries. The differences in the percentage of stunted children were estimated for each year of age and sex. The z scores of body mass index-for-age and weight-for-height were calculated with the use of the WHO and NCHS references, respectively, to compare differences in the prevalence of thinness and wasting. RESULTS: No systematic differences in mean z scores of height-for-age were observed between the WHO and NCHS growth references. However, z scores of height-for-age varied by sex and age, particularly during early adolescence. In children for whom weight-for-height could be calculated, the estimated prevalence of thinness (WHO reference) was consistently higher than the prevalence of wasting (NCHS reference) by as much as 9% in girls and 18% in boys. CONCLUSIONS: In undernourished populations, the application of the WHO (2007) references may result in differences in the prevalence of stunting for each sex compared with results shown when the NCHS references are used as well as a higher estimated prevalence of thinness than of wasting. An awareness of these differences is important for comparative studies or the evaluation of programs. For school-age children and adolescents across all ranges of anthropometric status, the same growth references should be applied when such studies are undertaken.