Ethnographic data and archeological censuses of cities suggest that sub-Saharan Africa lagged behind tropical America during pre-colonial times. Disease (i.e., environmentally determined pathogen stress) has a negative impact on pre-colonial economic conditions, as measured by the presence of large physical structures in ethnographic data. This negative relationship is seen primarily, but not exclusively in African societies. Using a simple coalitional game, I propose a causal path from disease to ethnic diversity. Ethnographic data suggests a positive effect of disease on ethnic diversity, and persistent effects on long-term economic development. Even today, pre-colonial factors influence income per capita and ethnolinguistic fractionalization.