OBJECTIVE: The present study analysed the impact of using the 2006 WHO Child Growth Standards ('the WHO standards') compared with the 1977 National Center for Health Statistics (NCHS) international growth reference ('the NCHS reference') on the calculated prevalence of chronic malnutrition in children aged 6·0-59·9 months. DESIGN: Anthropometric data were collected as part of a cross-sectional study exploring the association between household environments and nutritional status of children. Z-scores were computed for height-for-age (HAZ), weight-for-age (WAZ) and weight-for-height (WHZ) using each reference/standard. Results were compared using Bland-Altman plots, percentage agreement, kappa statistics, line graphs and proportion of children in Z-score categories. SETTING: The study was conducted in thirteen rural villages within Honduras's department of Intibucá. SUBJECTS: Children aged 6·0-59·9 months were the focus of the analysis, and households with children in this age range served as the sampling unit for the study. RESULTS: The WHO standards yielded lower means for HAZ and higher means for WAZ and WHZ compared with the NCHS reference. The WHO standards and NCHS reference showed good agreement between Z-score categories, except for HAZ among males aged 24·0-35·9 months and WHZ among males aged >24·0 months. Using the WHO standards resulted in higher proportions of stunting (low HAZ) and overweight (high WHZ) and lower proportions of underweight (low WAZ). The degree of difference among these measures varied by age and gender. CONCLUSIONS: The choice of growth reference/standard employed in nutritional surveys may have important methodological and policy implications. While ostensibly comparable, data on nutritional indicators derived with different growth references/standards must be interpreted cautiously.