Background: This study aims to understand the determinants of the Global Fund to Fight AIDS, Tuberculosis, and Malaria's dedicated channel for health systems strengthening (HSS) funding across countries and to analyze their health system priorities expressed in budgets and performance indicators. Methods: We obtained publicly available data for disease-specific and HSS grants from the Global Fund over 2004-2013 prior to the new funding model. Regression analysis was employed to assess the determinants of dedicated HSS funding across 111 countries. Documents for 27 dedicated HSS grants including budgets and performance indicators were collected, and activities were analyzed by health system functions. Results: HSS funding per capita is significantly associated with TB and HIV funding per capita, but not per capita income and health worker density. Of 27 dedicated HSS grants, 11 had line-item budgets publicly available, in which health workforce and medical products form the majority (89% or US$132 million of US$148 million) of funds. Yet these areas accounted for 41.7% (215) of total 516 performance indicators. Conclusions: Health worker densities were not correlated with HSS funding, despite the emphasis on health workforce in budgets and performance indicators. Priorities in health systems in line-item budgets differ from the numbers of indicators used.
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