The global malaria burden has dramatically decreased in recent years, with at least four million fewer deaths today compared to 2001. WHO has estimated that between 2000 and 2015, the annual rate of new malaria cases dropped by 37% globally, and malaria death rates fell by 60%. Current vector control practices, notably long-lasting insecticide treated nets (LLINs) and indoor residual sprays (IRS) have contributed to a significant proportion of this reduction, but the progress is now leveling off, as these interventions are reaching their fundamental protective limits. In many settings, low-level residual transmission now persists even where LLIN and IRS coverage already exceeds 80%. This problem is compounded by the widespread lack of accurate data on the extents and drivers of this residual transmission. We have identified two critically urgent needs associated with this phenomenon as follows: First, it is essential to exhaustively investigate the actual magnitude of the residual malaria transmission, and characterize it on the basis of where and when it occurs, as well as its main environmental and anthropological determinants in different ecological and epidemiological settings. Second, we need complementary interventions, and improved surveillance-response strategies, to effectively target the residual transmission and monitor progress towards elimination. We will rapidly and exhaustively address the first of the above concerns, and then make actionable recommendations for the second. The main objective of this study is therefore to quantify and characterize existing residual Plasmodium transmission in communities where LLINs are already widely used, but where transmission still persists. In the short-term, we will deliver a set of profiles and quantifications of residual malaria transmission and its associated determinants in selected sites in Burkina Faso and Tanzania. This will then enable effective targeting for malaria elimination. To achieve this main aim, we will pursue the following specific activities.