We conducted a needs assessment that describes the landscape of civil society organizations (CSOs) in three informal settlements around Nairobi, Kenya. The numbers of CSOs have rapidly increased in areas underserved by governments including poor urban neighbourhoods but little is known about CSOs capacity to meet the priority health needs of the urban poor. It is also unclear why, despite a proliferation of CSOs, residents still experience unimproved health outcomes. We collected data on core activities, financial management, and governance structures. Of the 952 CSOs assessed, 47 per cent reported HIV/AIDS counselling, prevention, and treatment as their core activity. Most CSOs reported good financial management systems and governance structures but responses were not validated. Representation in district health stakeholder fora was low; most CSOs did not have the capacity to effectively deliver services that would have impact. For CSOs to realize the desired goal to improve the well-being of low-income populations, programmes to build their management capacity are essential.