Intermittent food insecurity due to drought and the effects of HIV/AIDS affect child nutritional status in sub-Saharan Africa. In Southern Africa in 2001-3 drought and HIV were previously shown to interact to cause substantial deterioration in child nutrition. With additional data available from Southern and Eastern Africa, the size of the effects of drought and HIV on child underweight up to 2006 were estimated. To determine short- and long-term trends in child malnutrition in Eastern and Southern Africa and how these are affected by drought and HIV. A secondary epidemiologic analysis was conducted of area-level data derived from national surveys, generally from the mid-1990s to the mid-2000s. Data from countries in the Horn of Africa (Ethiopia, Kenya, and Uganda) and Southern Africa (Lesotho, Malawi, Mozambique, Swaziland, Zambia, and Zimbabwe) were compiled from available survey results. Secondary data were obtained on weight-for-age for preschool children, HIV prevalence data were derived from antenatal clinic surveillance, and food security data were obtained from United Nations sources (Food and Agriculture Organization, International Labour Office, and others). Overall trends in child nutrition are improving as national averages; the improvement is slowed but not stopped by the effects of intermittent droughts. In Southern Africa, the prevalence rates of underweight showed signs of recovery from the 2001-03 crisis. As expected, food production and price indicators were related (although weakly) to changes in malnutrition prevalence; the association was strongest between changes in food production and price indicators and changes in malnutrition prevalence in the following year. Areas of higher HIV prevalence had better nutrition (in both country groups), but this counterintuitive association is removed after controlling for socioeconomic status. In low-HIV areas in Eastern Africa, nutrition deteriorates during drought, with prevalence rates of underweight 5 to 12 percentage points higher than in nondrought periods; less difference was seen in high-HIV areas, in contrast to Southern Africa, where drought and HIV together interact to produce higher prevalence rates of underweight. Despite severe intermittent droughts and the HIV/AIDS epidemic (now declining but still with very high prevalence rates), underlying trends in child underweight are improving when drought is absent: resilience may be better than feared. Preventing effects of drought and HIV could release potential for improvement and, when supported by national nutrition programs, help to accelerate the rates of improvement, now generally averaging around 0.3 percentage points per year, to those needed to meet Millennium Development Goals (0.4 to 0.9 percentage points per year).