Anaemia remains the most prevalent nutritional disorder among women and children in the Middle East and North Africa region. We examined anaemia trends using data from the Egyptian Demographic and Health Surveys. Between 2000 and 2005, the prevalence of anaemia (defined as haemoglobin concentrations <11 g dL−1) increased from 37.04% to over 52% among Egyptian children between 12 months and 36 months of age. We examined the associations of these changes with food consumption, vitamin A administration, recent illness, immunization status, socio-demographic factors and a child's anaemic status. Children under the age of 24 months who had recently been sick and those who resided in Upper Egypt were significantly more likely to be anaemic. Despite significant improvements in water and sanitation facilities, maternal education and asset-based household wealth, there were marked declines in the consumption of nutritive foods and increases in the prevalence of childhood diarrhoea between 2000 and 2005. Placing these analyses in the broader context of Egyptian economic trends suggests that the nutritional basket consumed by Egyptian households between 2000 and 2005 may have shifted towards less nutritive foods with lower costs per calorie, probably in response to economic difficulties and increasing food prices. Shifts in dietary consumption, in conjunction with increases in diarrhoea, are likely contributing to the rapid increase in childhood anaemia in Egypt between 2000 and 2005. National-level fortification efforts may be one way to combat rising levels of anaemia among Egyptian women and children.