The burden of malaria is a key challenge to both human and economic development in malaria endemic countries. The impact of malaria can be categorized from three dimensions, namely: health, social and economic. The objective of this study was to estimate the impact of malaria morbidity on gross domestic product (GDP) of Uganda.The impact of malaria morbidity on GDP of Uganda was estimated using double-log econometric model. The 1997-2003 time series macro-data used in the analysis were for 28 quarters, i.e. 7 years times 4 quarters per year. It was obtained from national and international secondary sources.The slope coefficient for Malaria Index (M) was -0.00767; which indicates that when malaria morbidity increases by one unit, while holding all other explanatory variables constant, per capita GDP decreases by US$0.00767 per year. In 2003 Uganda lost US$ 49,825,003 of GDP due to malaria morbidity. Dividing the total loss of US$49.8 million by a population of 25,827,000 yields a loss in GDP of US$1.93 per person in Uganda in 2003. Malaria morbidity results in a substantive loss in GDP of Uganda. The high burden of malaria leads to decreased long-term economic growth, and works against poverty eradication efforts and socioeconomic development of the country.