Botswana has the second highest HIV prevalence rate and highest rate of orphanhood in the world. Although child mortality rates have doubled in 15 years, the extent to which health disparities are connected to orphan status remains unclear. We conducted an analysis of the 2000 Botswana Multiple Indicator Cluster Survey to examine whether orphan-based health disparities exist. We measured health inequalities using anthropometric data among 2723 under-five year olds, nested in 1854 households, and 208 communities. We calculated multilevel logistic regression models to estimate the child, household, and regional determinants of growth failure. We found that orphaned children aged 0-4 are 49% more likely to be underweight than nonorphans (p<0.05) controlling for household poverty and other factors; and orphans disproportionately live in the poorest households. Throughout sub-Saharan Africa (SSA), Botswana is a leader in responding to the AIDS epidemic, in particular as one of the first countries to offer universal antiretroviral treatment. However, orphan-based health disparities confirm that the orphan response is still insufficient. Better data are needed to fully understand the mechanisms that lead to these disparities, and the public sector needs an increased capacity to fully implement the policies and programs designed to meet the needs of orphans. Findings from this study have important implications for countries throughout SSA, and Southern Africa in particular, where the number of orphans has doubled to tripled over the past 15 years.