Machu Picchu and the Amazon are two different trips. Plan them that way.

Most first trips to Peru run from Lima to Cusco, through the Sacred Valley and on to Machu Picchu by the Inca Trail or the train. Mosquito-borne disease barely touches that route. The city of Cusco sits at about 11,200 ft (3,400 m), too high for the dengue mosquito, and the CDC lists no malaria for Cusco, Machu Picchu or Lima. Add a few nights at a lodge near Puerto Maldonado or Iquitos and the checklist changes. Dengue, meanwhile, has doubled from 2025, mostly on the north coast and in the Amazon.

Two trips, two sets of rules

Elevation draws the line. The CDC's malaria area is everything below 8,200 ft (2,500 m) east of the Andes, and its yellow fever vaccine recommendation covers areas below 7,550 ft (2,300 m) in the Amazon regions. The highland tourist areas fall outside both.

Machu Picchu's biting flies

The bites people bring home from the highlands usually come from Machu Picchu itself. Travelers widely report tiny biting flies on the grass terraces and call them sand flies. The bites often go unnoticed at the time and itch for days, and the flies work in daylight all year, exactly when you're on the site.

Long trousers and sleeves, repellent on any exposed skin (ankles, neck, hands) and staying off the grass prevent most of them. Cusco and Lake Titicaca tend to be too high and cold for mosquitoes to be much of a problem.

Aguas Calientes, the town below Machu Picchu, sits lower, at about 6,600 ft (2,000 m), and its outdoor restaurants have a reputation for mosquitoes at dusk. The CDC's Peru page doesn't name the town. By elevation it falls below both the malaria and yellow fever cutoffs, while the CDC explicitly excludes Machu Picchu just above it. If you're spending a night there, ask the travel clinic to check it against the CDC's maps, and wear repellent to dinner either way.

The Amazon: malaria and yellow fever

Peru's Amazon trips start from Iquitos, in the Loreto region, or from Puerto Maldonado in Madre de Dios, the base for the Tambopata lodges. Both cities are inside the CDC's malaria area. Most cases are P. vivax, a fifth are the more dangerous P. falciparum, and the parasite resists chloroquine, so the CDC lists other prevention medicines.

The CDC also recommends yellow fever vaccine for travelers 9 months and older going to areas below 7,550 ft (2,300 m) in Amazonas, Cusco, Huánuco, Junín, Loreto, Madre de Dios, Pasco, Puno, San Martín and Ucayali, plus designated areas of several other regions. PAHO counted 49 confirmed cases and 19 deaths in Peru in 2025, most in Amazonas and San Martín, and two more cases were confirmed in Madre de Dios in the first seven weeks of 2026. Peru does not require the vaccine for entry.

Malaria mosquitoes bite from dusk to dawn, as do the sand flies behind leishmaniasis, which the CDC also lists for Peru. Permethrin-treated clothing, repellent at sunset and the lodge's bed net cover both. Oropouche, a virus spread mainly by a tiny biting midge, is present in the Amazon too. PAHO counted 330 confirmed cases in Peru through mid-July 2025, about half of them in Loreto. Our biting-midge guide explains how midges behave. The CDC's Peru page also lists New World screwworm, a fly that lays eggs in wounds, and advises cleaning and covering any cut.

Dengue doubled in 2026

By mid-September 2026, the Pan American Health Organization counted 63,407 dengue cases in Peru, double the same period of 2025. Severe cases rose 55% and deaths 39%, to 71, with the DENV-3 type most common. Early in the year the hardest-hit regions were San Martín, Ucayali and Loreto in the Amazon, the Peruvian press reported, and on the north coast, Piura region has reported about 13,000 cases this year.

In Lima, the DIRIS Lima Centro health network reported 1,201 locally acquired cases by late July, 1,095 of them in San Juan de Lurigancho, an outer district. Those figures don't cover all of the city. Peru is not on the CDC's global dengue notice list, last reviewed in early October, so check it again before you fly.

The dengue mosquito, Aedes aegypti, bites in daylight, with peaks after sunrise and before sunset, so on the coast and in the Amazon repellent goes on over sunscreen in the morning and again in the late afternoon. Our dengue & Zika daily routine has the full schedule. The CDC's Peru page also lists Zika, which can pass from a pregnant woman to her baby, and elevated chikungunya risk, with vaccination to be considered for stays of six months or more. Raise either at the clinic if it applies.

Where you're going

Here is how the main stops compare in any month.

When to go

June to September is the Andean dry season and, in a normal year, the low point for dengue on the coast, which makes it the easiest stretch overall. January to May is the hard season on the north coast and in the Amazon, when rain and heat drive dengue. Normally Peru's cases peak between January and June and start climbing again in the year's last weeks.

This year broke that pattern. Cases rose from early March and were still running at double 2025's level in September, a rise PAHO links to El Niño. Its October update warns that El Niño is expected to intensify as South America's peak season approaches. For a December–May trip to Máncora or the Amazon, that makes the daytime routine more important than usual. Cusco, the Sacred Valley and Lake Titicaca are low-risk in any month, and Machu Picchu's flies bite all year.

What travelers report

Paraphrased from forum threads and reviews and linked so you can read them in full. None of them gives a year, and individual trips vary with season, weather and where you stay.

• Machu Picchu

  Replies to a traveler worried about sand flies said experiences vary widely: some got no bites, while others found bites hours or days later without noticing anything at the site. The advice was long sleeves and pants, repellent on exposed skin, staying off the grass terraces where the flies gather, and carrying antihistamines. TripAdvisor ↗

• Machu Picchu (site review)

  A reviewer of the Machu Picchu site led the review with a warning to beware of the sand flies. TripAdvisor ↗

• Sacred Valley

  In a thread about sand flies and mosquitoes in the Sacred Valley, a reply said visitors will find mosquitoes, but more at Machu Picchu than in the Sacred Valley. TripAdvisor ↗

• Chuncho Lodge, Tambopata

  A guest had almost no mosquitoes during the stay, but noted that the guide put this down to luck and nature rather than the norm. TripAdvisor ↗

• Tambopata Ecolodge

  A guest who liked the lodge said the rainforest was very hot and humid, with a lot of mosquitoes and other biting flies. TripAdvisor ↗

• Tambopata (Madre de Dios)

  In an older thread, a poster disputed a lodge's claim that the area had been malaria-free for 20 years, citing a Ministry of Health bulletin that listed malaria cases in Tambopata. TripAdvisor ↗

One more rule outlasts the trip. Any fever during or after your trip means a doctor visit, and you tell them you were in Peru and which regions you visited. Dengue usually shows up within two weeks; malaria can take longer. That one sentence is what gets you the right test quickly.

Traveler questions