As donors have scaled up efforts to improve health in sub-Saharan African, African countries have diverged sharply in their health performance: Some countries have made rapid progress while others have stagnated. Yet the reasons for these divergences are often not well understood. In this dissertation I present in-depth case studies of two such divergent countries, Tanzania and Uganda, over the 1995-2007 period. Over this period, Tanzania reduced its under-5 mortality rate by 35%, while Uganda’s mortality rate decline was less than half as rapid; between 12% and 15% over virtually the same period. This occurred despite the fact that both countries received similar amounts of foreign aid for health, implemented virtually identical health sector reforms, and saw comparable rates of growth in GDP per capita and similar trends in other socioeconomic indicators. Explanations for such differences often vary by academic discipline. Public health scholars often focus on coverage levels of critical child health interventions, while political scientists emphasize variation in the quality of governance institutions. I show that coverage of child survival interventions did indeed differ between Tanzania and Uganda, particularly in the area of malaria control, but that the ultimate determinant of these differences can be traced to political economy factors. Specifically, regime maintenance dynamics and the differing composition of political patronage coalitions in the two countries determined the relative success of health sector programming in Tanzania and Uganda.