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Research into the effects of global health initiatives (GHIs) on health systems has largely left out the viewpoints and contributions of civil society. This study details civil society's perspective regarding the effects of two GHIs, the US President's Emergency Plan for AIDS Relief (PEPFAR) and the Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), on country health systems and the added value of civil society interacting with GHIs to strengthen health systems. The study employed qualitative data collection methods using semi-structured interviews administered during focus groups and key informant interviews. A range of health system stakeholders were interviewed in Kenya, Malawi, Uganda and Zambia. Data were coded and analysed for themes and sub-themes. In total, 2910 civil society participants provided information individually or in focus groups. Respondents reported that GHIs have contributed to dramatic health benefits within and outside of a disease-specific focus, including health systems strengthening efforts. However, opportunities for synergy between GHIs and health systems have been missed, and GHIs have not worked sufficiently to close capacity gaps of grassroots civil society organisations. Despite some governance innovations, civil society's opportunities to participate meaningfully in GHI priority setting efforts are limited. Recommendations are included on how to best use GHIs to strengthen health systems by partnering with civil society.