Atovaquone and proguanil are medications to treat malaria, a disease caused by parasites. These medicines work by interfering with the growth of parasites in the red blood cells of the human body. Parasites that cause malaria typically enter the body through the bite of a mosquito. Malaria is common in areas such as Africa, South America, and Southern Asia. The combination of atovaquone and proguanil is used to treat or prevent malaria. Atovaquone and proguanil may also be used for purposes not listed in this medication guide.