Somalia is considered the most fragile of the fragile states: more than fifteen years of war and cyclical natural catastrophes have placed an immense burden on millions of Somalis. Displacement, famine, droughts, disease outbreaks, and illiteracy have become the norm. The international community has tried to respond to Somalia's tragedy and over the years has allocated substantial amounts of funds to a variety of sectors to help address this chronic emergency. This paper focuses on aid financing to the health sector over the period 2000 to 2006. It thoroughly reviews the flows of funds in the complex aid architecture of the Somalia health sector. The study on the 2000-06 aid flows to the health sector in Somalia is a first attempt to fill a large gap of knowledge in this area. The primary objectives of the study were to assess how levels of donor financing varied over the years; which health interventions were prioritized by donors; and how evenly health sector aid was distributed to the different zones of Somalia. The overall aim of the study was to create evidence for donors, implementers and health specialists involved in allocation of financial resources to the Somali health sector.