Many of the world's poorest people live in areas with high malaria rates and suffer the associated physical, economic and social hardships. These same areas are often undergoing extensive forest conversion and degradation. While causality has generally not been established, the scientific literature makes it abundantly clear that the juxtaposition of deprivation, deforestation and disease is not pure coincidence. We chart a course for using transdisciplinary research to develop more effective policies to control malaria, protect forests and alleviate poverty. The paper concludes with a proposal for strategically linking research and policy at the malaria-deforestation-poverty nexus in a comprehensive decision-analysis framework that channels research to the most pressing policy needs, informs policy with the most conclusive research and ensures stakeholders are effectively informed about their options.