BACKGROUND: The HIV epidemic has triggered the development of new health institutions with a special focus on HIV care. The role of these relatively new institutions within the health systems of low-income countries like Malawi is not clearly determined. We evaluate and describe the development of one example, the Lighthouse Trust (Lighthouse), over a period of 15 years (2000-2015). METHODS: Data from multiple sources, including a document review, participatory observation and interviews were analysed, triangulated and synthesized. The institution's development, function, cooperation, financing, research and training were analysed using institutional administrative documents, annual reviews, project reports. For the assessment of the research activities, all publications that the Lighthouse contributed to were retrieved and categorized. Participatory observation and interviews with key Lighthouse staff members and external stakeholders were conducted. RESULTS: Established in 1997 as a volunteer initiative for home-based care, the Lighthouse has developed considerably. Major steps include being registered as a trust, moving into their own buildings, expanding clinical services, becoming a centre for clinical service, training and research working with close to 300 employees. As an independent legal entity, Lighthouse Trust works in close cooperation with Malawian public health services and plays an important role in the government's HIV programme. Funding comes from various sources with a lion's share from the US Centers for Disease Control and Prevention. Throughout 2015, the Lighthouse performed 58,210 HIV testing and counselling encounters and by year's end, 28,302 patients were alive and on ART. From 2000 to 2015 Lighthouse staff contributed to 94 peer-reviewed publications. CONCLUSION: Novel institutions like the Lighthouse have been developed in the response to HIV. The Lighthouse has demonstrated its capacity to deliver health services and contributed significantly to the current level of success in addressing the disease. However, this kind of institution's position in local health care systems is still developing. The Lighthouse will need to continue to work on well-planned strategies that consider the changing landscape of health needs, health care provision and financing. Independent institutions like the Lighthouse can contribute to the development of health systems in countries like Malawi that improve health care responsiveness and quality for the entire population.