Cross-sectional data for breastfed infants in rural Zambia were used to evaluate the effect of applying two different data sets as a reference, i.e. the WHO 12-month breastfed pooled data set and the National Center for Health Statistics (NCHS) growth reference in terms of prevalence of malnutrition (stunting, underweight, and wasting). A total of 518 infants who were attending mother-and-child health clinics were included. Age, weight and length were recorded. Anthropometric Z-scores were calculated in two ways: by applying the NCHS growth reference and by using the WHO breastfed data set. Anthropometric Z-scores calculated using the breastfed data set were lower during the first 6–7 months of life compared with those calculated by applying the NCHS growth reference. This resulted in a higher proportion of children aged 0–6 months being classified as stunted and underweight using the breastfed data set versus the NCHS growth reference. After the age of 7 months, similar prevalences of stunting or underweight were observed. Relatively few infants were classified as wasted. In order to adequately assess the prevalence of stunting and underweight in breastfed infants, it is recommended that a new growth reference be developed, as has been initiated by WHO.