We examined the difference in the prevalence estimates of the outcome indicators for the new World Health Organization (WHO) child growth standard reference (WHO 2006) and the National Center for Health Statistics (NCHS)/WHO reference using the National Protein-Energy Malnutrition Survey dataset. Based on the NCHS/WHO reference, overall prevalence estimates of underweight, wasting, stunting and overweight were 17.8%, 7.4%, 10.9% and 1.3% compared to 11.3%, 7.6%, 13.0% and 1.9% respectively calculated according to the WHO 2006 reference: stunting and overweight showed statistically significantly higher estimates, whereas underweight was statistically significantly lower. The differences were not consistent across age groups.