BACKGROUND: Ministers of health, donor agencies, philanthropists, and international agencies will meet at Bamako, Mali, in November, 2008, to review global priorities for health research. These individuals and organisations previously set health priorities for WHO, either through its regular budget or extra-budgetary funds. We asked what insights can be gained as to their priorities from previous decisions within the context of WHO. METHODS: We compared the WHO biennial budgetary allocations with the burden of disease from 1994-95 to 2008-09. We obtained data from publicly available WHO sources and examined whether WHO allocations varied with the burden of disease (defined by death and disability-adjusted life years) by comparing two WHO regions-Western Pacific and Africa-that are at differing stages of epidemiological transition. We further assessed whether the allocations differed on the basis of the source of funds (assessed and voluntary contributions) and the mechanism for deciding how funds were spent. FINDINGS: We noted that WHO budget allocations were heavily skewed toward infectious diseases. In 2006-07, WHO allocated 87% of its total budget to infectious diseases, 12% to non-communicable diseases, and less than 1% to injuries and violence. We recorded a similar distribution of funding in Africa, where nearly three-quarters of mortality is from infectious disease, and in Western Pacific, where three-quarters of mortality is from non-communicable disease. In both regions, injuries received only 1% of total resources. The skew towards infectious diseases was substantially greater for the WHO extra-budget, which is allocated by donors and has risen greatly in recent years, than for the WHO regular budget, which is decided on by member states through democratic mechanisms and has been held at zero nominal growth. INTERPRETATION: Decision makers at Bamako should consider the implications of the present misalignment of global health priorities and disease burden for health research worldwide. Funds allocated by external donors substantially differ from those allocated by WHO member states. The meeting at Bamako provides an opportunity to consider how this disparity might be addressed.