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Malaria is prevalent in many parts of Rwanda and it would be difficult to holiday there without some risk of exposure. That said, Volcanoes National Park and the associated gorilla-tracking trailheads and lodges all lie at too high an altitude for malaria to be much of a risk, as does Nyungwe National Park, though in both cases you would need to pass through medium- to high-risk areas to get there from Kigali. The risk of malaria is far higher in the relatively low-lying Akagera National Park and along the shores if Lake Kivu.
