Significance
In the wake of the 2015–2016 El Niño, multiple cholera epidemics occurred in East Africa, including the largest outbreak since the 1997–1998 El Niño in Tanzania, suggesting a link between El Niño and cholera in Africa. However, little evidence exists for this link. Using high-resolution mapping techniques, we found the cholera burden shifts to East Africa during and following El Niño events. Throughout Africa, cholera incidence increased three-fold in El Niño-sensitive regions, and 177 million people experienced an increase in cholera incidence. Without treatment, the case fatality rate can reach 50%, but accessible, appropriate care nearly eliminates mortality. Climatic forecasts predicting El Niño events 6–12 mo in advance could trigger public health preparations and save lives.