Staying healthy in Ecuador depends on where in Ecuador you go. Most Ecuador trips move between Quito and the Andes at altitude, the Amazon lowlands east of the mountains, and the Galápagos Islands, and questions about malaria in Ecuador or which vaccines you need have a different answer for each. Our travel consultants are not medical professionals and cannot give medical advice. The US CDC advises seeing your doctor or a travel clinic at least a month before your trip. Take your itinerary along: the province and the altitude change the answer.
The CDC’s Ecuador page asks every traveler to be up to date on routine vaccines, including measles. It recommends hepatitis A for unvaccinated travelers one year and older and hepatitis B for unvaccinated travelers under 60, and suggests considering typhoid for rural areas or longer stays. On rabies, the CDC notes that vaccine after a bite may only be available in larger cities, and advises deciding on a pre-trip vaccine with your doctor.
The CDC maps yellow fever and malaria by region:
| Area | Yellow fever vaccine (CDC) | Malaria (CDC) |
|---|---|---|
| Quito, Cuenca and the Andes above 7,550 ft (2,300 m) | Not recommended | None in Quito; malaria listed only below 5,000 ft (1,500 m) |
| East of the Andes below 7,550 ft, including the Amazon (Morona-Santiago, Napo, Orellana, Pastaza, Sucumbíos, Tungurahua, Zamora-Chinchipe) | Recommended from 9 months of age | Below 5,000 ft in Morona-Santiago, Orellana, Pastaza and Sucumbíos; rare elsewhere |
| Pacific coast and western lowlands | Generally not recommended; not for Guayaquil | Below 5,000 ft in Esmeraldas and Cotopaxi provinces; none in Guayaquil |
| Galápagos Islands | Not recommended | None |
In the six provinces where the CDC lists malaria, it recommends prescription medicine to prevent it and asks travelers to talk to their doctor about which one to take; elsewhere, bite prevention only. Orellana, in the Amazon, is one of them. The Napo Wildlife Center tour flies from Quito to Coca, the capital of Orellana province, then goes about two hours by motorboat and two more by canoe into Yasuní National Park.
From May to August 2025 Ecuador required a yellow fever certificate from travelers arriving from Colombia, Peru, Bolivia and Brazil. On August 28, 2025, Ecuador’s Ministry of Public Health dropped that requirement and made the vaccine a recommendation, especially for travelers heading into jungle areas, given at least ten days before travel. Some official listings, the CDC’s included, still show a certificate for certain arrivals, so if your trip combines Ecuador with another country, confirm the current rule with your airline or Ecuador’s consulate. For your own protection, the CDC recommendation is in the table above. Other entry paperwork is on our Ecuador visa requirements page.
Quito sits at 9,350 ft (2,850 m), and our mainland trips usually begin there. The CDC Yellow Book says unacclimatized travelers sleeping at 8,000 ft or higher can develop altitude illness, and advises against going from below 4,000 ft to a sleeping altitude above 9,000 ft in one day. A flight into Quito does exactly that. Where such an abrupt ascent cannot be avoided, the Yellow Book suggests acetazolamide to speed acclimatization, so some travelers ask their doctor about it.
For the first 48 hours, the Yellow Book advises only mild exercise and no alcohol. The Quito, Cuenca and Avenue of the Volcanoes tour starts gently: an arrival day, then a Quito city tour. Cotopaxi National Park, below the 19,347 ft (5,897 m) volcano, comes on day five, and the trip ends in Cuenca at 8,400 ft (2,560 m). The CDC also asks travelers to be especially careful with the sun at high elevation: sunscreen of at least SPF 15, protective clothing, shade at midday.
Beyond malaria and yellow fever, the CDC’s Ecuador page lists dengue, Zika and chikungunya, spread by mosquitoes, and notes that an infected pregnant woman can pass Zika to her unborn baby. As of November 2026, the CDC has global travel health notices for dengue and measles on that page; check it for the current status. For bite prevention, the CDC recommends an EPA-registered repellent with DEET, picaridin, IR3535, oil of lemon eucalyptus, PMD or 2-undecanone, loose long-sleeved shirts and long pants, and permethrin-treated clothing (never applied to skin).
The US CDC’s general advice for travelers is to choose factory-sealed drinks wherever tap water might be contaminated, and to skip ice where clean water is a concern. For what to eat, from highland soups to coastal ceviche, see our Ecuador food and drink guide.
From an Amazon lodge, a clinic is a canoe, a boat and a flight away. The UK Foreign Office notes that medical facilities in the Galápagos Islands are limited, that Isabela has only a very basic health center, and that travel insurance should include air ambulance evacuation; the CDC suggests considering medical evacuation insurance. See our Ecuador travel insurance page and, for the islands and the boats, the Galápagos health guide.
According to the CDC, yes: below 5,000 ft in six provinces, including the Amazon provinces of Morona-Santiago, Orellana, Pastaza and Sucumbíos, and none in Quito, Guayaquil or the Galápagos.
In August 2025 Ecuador’s Ministry of Public Health dropped its certificate rule for arrivals from Colombia, Peru, Bolivia and Brazil; if your trip includes another country, confirm the current rule with your airline. For protection, the CDC recommends the vaccine for the Amazon and other areas below 7,550 ft east of the Andes.
About 9,350 ft (2,850 m), and Cuenca about 8,400 ft (2,560 m). Both are above the 8,000 ft sleeping altitude at which the CDC Yellow Book says unacclimatized travelers are at risk of altitude illness.
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