While the Cayo normally has relatively few mosquitoes, thanks to the porous limestone terrain that doesn't allow water to stand in puddles, there are occasional outbreaks of dengue fever. Dengue, which causes flulike symptoms, and, in more serious cases, death from internal bleeding, is transmitted by the bite of Aedes aegypti and Aedes albopictus mosquitoes. The Zika virus is also present in mosquitoes in Belize; Zika causes a rash and flulike symptoms as well as microcephaly in newborn babies when infected during pregnancy. These species of mosquitoes that carry Zika are most active in the early morning and late afternoon. Travelers, especially during the rainy season, should consider using insect repellent with DEET. There is as yet no preventative medicine for dengue or for Zika, although vaccines for both are currently under development. Pay close attention to travel warnings, and avoid travel to this region if you are pregnant or are thinking of becoming pregnant.

Health standards in the Cayo are high. The water in San Ignacio and Santa Elena comes from a treated municipal system, so it's safe to drink, though many people prefer the taste of bottled water. Resorts in the region have their own safe water systems.

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