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COVID-19 has caused significant morbidity and mortality, both directly and indirectly via the disruption to routine health services. Evidence on the indirect health impacts has largely been anecdotal or modeled, and cause/program-specific. We aimed to document the indirect health impacts in four countries with different experiences: Kenya, the Philippines, South Africa, and Uganda. Using a common framework that encourages a whole-of-health assessment of the indirect health impacts of COVID-19, we used a variety of data sources, including estimates of excess mortality and changes in service utilization and coverage, to analyze the impacts of COVID-19 and its response measures on key health conditions and services. We found that each country experienced disruptions to health services, but the disruptions varied in terms of the services, geographic areas, and subpopulations affected, and most importantly, the degree and duration of disruptions experienced. We must continue to routinely and systematically measure the health and socioeconomic impacts of both the virus and the control measures, with short-, medium- and long-term timeframes and with an equity lens to look at how the virus has differentially impacted societal groups.