Malaria is one of the deadliest infectious diseases in the world causing significant mortality and morbidity. This inflicts a heavy social and economic burden on the affected developing countries. There is an urgent need for the development of new drugs for malaria as the efficancy of current gold-standards is dramatically decreasing due to the emergence of drug resistant parasites. The disease pathology results from the blood stage of the parasite’s complex lifecycle and is initiated when merozoites, the extracellular invasive forms, invade red blood cells. The invasion process is rapid and the only time within the blood stage lifecycle where the parasite is directly exposed to the immune system. Therefore merozoite invasion has been considered as a potential weak point of the lifecycle and extensive research has been focused on merozoite invasion as a target for the development of blood stage malaria vaccine. We aim to dissect the exact timing of invasion events in malaria parasites using nano scale imaging techniques in order to investigate how, when and where potential vaccine candidates are exposed to the immune system during invasion. The combination of correlative light and electron microscopy as well as focussed ion beam (FIB-SEM) allows us to assemble an accurate and detailed 3D map of protein localisations and organelle behaviour during invasion. This therefore enables investigation of the exact consequences of blocking release of invasion organelles. This serves as a new platform to test inhibitors that block organelle realease, and therefore a screen for drugs and vaccines that stop malaria parasites from invading human cells. The outlined techniques will pinpoint the timing and route of invasion content release and facilitate a more detailed understanding of invasion cell biology.