A project management unit (PMU) was established to manage the implementation of the grant.

Timor-Leste has been awarded five Global Fund grants: the malaria grant in 2003; a TB grant in 2005 which was suspended in 2006; an HIV/AIDS grant in 2006; and second grants for TB and malaria in 2009. The focus of this study is on the first Global Fund grant for national malaria programme from 2003 to 2006.

This study describes the results produced through the Global Fund supported programme on malaria control, analyses whether Timor-Leste abided by the Global Fund's *principle of additionality*, and examines the impact of the Global Fund on national malaria control and the health system, as well as the challenges faced during grant implementation.

It is worthwhile to note some terminologies are usedquantitative data analysis was directed at analysing the annual malaria incidence (AMI) rates from 2004 to 2008. This was calculated using the total annual malaria cases from 2004 to 2008 divided by the total population and multiplied by 1,000. The total yearly malaria cases of 2004 to 2008 was obtained from the Ministry of Health and the data on population numbers (924,624) were obtained from the 2004's Census Report \[[@B11]\], with a projection of annual population growth of 3.13 % \[[@B12]\] to take account of the increase of population numbers in the subsequent years after 2004.

Since the objective of the Global Fund funded malaria programme was to reduce malaria morbidity and mortality by 30 % at the end of the project, the 2004's AMI was used as the baseline to