The Global Fund to fight HIV/AIDS, Tuberculosis and Malaria (GFATM) was founded in 2002 in the context of increased political and financial commitments towards health and development, in the aftermath of the Millennium Declaration, and on track to implement the Millennium Development Goals (MDGs). As of today, the institution has mobilized over 16 billion US dollars through its partnership, and spent over 8 billion dollars through 620 contracts in 140 countries for these three diseases. Principles at inception were to accelerate and expand HIV, TB, and Malaria prevention and awareness, care, and treatment related activities, in the poorest and the most affected countries worldwide, with a special emphasis on Africa, being the continent with the highest disease burden, especially with respect to HIV/AIDS and its dreadful social and economic consequences. In 2006, a Technical and Evaluation Reference Group was set up. This group responding to the GFATM Board in relation to the 5-year evaluation, defined the Terms of reference for the 5-year evaluation. Macro International, a firm based in Washington DC, was given the contract to conduct three studies over the period 2006-2009, looking at: (i) GFATM organizational effectiveness, (ii) partnerships at international and global levels, as well as systems effects, (iii) collective impact of the GFATM, the World Bank and (PEPFAR) funds on HIV, TB, and Malaria control. Twenty-five countries participated all together in the evaluation, out of which 18 in study area 3. Total budget for the evaluation amounted almost 17 million US dollars. This paper outlines: (i) the results of study areas 2 and 3 as well as the 5-year Evaluation Synthesis report, contents, and (ii) comments on the results and potential policy implications of the GFATM 5-year evaluation findings, as well as first responses prepared by the GF Secretariat shared at the GFATM Board meeting held in Ethiopia in November 2009. The evaluators raised the weaknesses of national health information systems, which limit the availability of reliable data and indicators that could be useful in assessing disease control impact as well as in monitoring the progress through management for result initiatives. Nevertheless, it can be shown that increased funding is linked to expansion of preventive interventions (including Voluntary Counseling and Testing (VCT) and preventing mother-to-child transmission (PMTCT)) as well as treatment (ARV) activities, the quality of which could be improved and better monitored. Especially in Eastern Africa, malaria control has improved significantly, benefiting from additional funding. Health systems' weaknesses at district level, such as human resources, laboratory commodities, and medicine shortages, are major constraints to further expansion of services and impact of funds. Issues at stake are the following: (i) soundness of the GFATM assumptions at inception with respect to national disease control strategies, especially in relation to HIV prevention, (ii) whether it belongs to the GFATM t...