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Clinical research on neglected tropical diseases is a challenge in low-resource countries, and the contribution of clinical and operational research to health system strengthening is poorly documented. Developing new, simple, safe, and effective treatments may improve the effectiveness of health systems, and conducting research directly in health structures may have an additional impact. This study describes the process of conducting clinical trials in the Democratic Republic of Congo (DRC) in compliance with international standards, and the role of the trials in strengthening health system functions, including governance, human resources, health information, provision of care, and the equipping of health services with the necessary supplies and infrastructure. We conclude that conducting clinical trials in endemic areas has not only reinforced and supported the aim of conducting high-level clinical research in endemic countries, but has also brought lasting benefits to researchers, staff, and hospitals, as well as to broader health systems, which have positive knock-on effect on patients outside of the clinical trials and their communities. Sustainability, however, remains a challenge in an underfunded health system, especially with respect to specialized equipment. Clinical research in most of sub-Saharan Africa is highly dependent on international input and external technical support; there are areas of weaknesses in trial design and documentation, as well as in data management and analysis. Financing remains a critical issue, as African investigators have difficulties in directly accessing sources of international research funding.