From February to May 2012, Mayotte experienced an outbreak of acute conjunctivitis with over 12,000 estimated cases, causing a significant burden on the primary healthcare system. It was most certainly caused by a coxsackievirus, as documented by isolation from a symptomatic traveller from the Comoros Islands in France. Tropical climate and poor hygiene conditions facilitate the spread of infectious diseases on Mayotte and in the region with risk of further exportation to mainland France and Europe.