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There is no vaccine, but prescription drugs help minimize your likelihood of contracting this mosquito-borne illness. Strains of malaria are resistant to the traditional regimen of chloroquine. There are three recommended alternatives: a weekly dose of mefloquine; a daily dose of doxycycline; or a daily dose of Malarone (atovaquone/proguanil). Any regimen must start before arrival and continue beyond departure. Ask your physician. Wear long sleeves and pants if you're out in the evening, and use a mosquito repellent containing DEET whenever you enter the jungle.
The Peruvian Embassy recommends getting a yellow fever vaccine at least 10 days before visiting the Amazon. Though recent cases of yellow fever have occurred only near Iquitos, southern Amazon lodges in Manu and Tambopata tend to be sticklers about seeing your yellow fever vaccination certificate. Carry it with you.