From the start of the refugee crisis it was apparent that malaria was the most serious health problem facing the displaced population. It was the first cause of death and represented over 45% of the out-patients consultations. Over 1% of all pregnant women died every year of severe and complicated falciparum infections. The region is hilly and forested and endemic for both Plasmodium falciparum and vivax. The incidence of P.falciparum increases with age but young children are more susceptible to severe infections. Pregnant women are particularly vulnerable to the complications of malaria infections that also reduce birthweight. P.vivax incidence decreases with age but its impact in pregnancy is not negligible. The transmission through the main vectors (A.dirus, A.minimus and A. maculatus) is low and unstable in this area, and epidemics are common. The major difficulty in the control of malaria is the high level of resistance in P.falciparum to almost all available compounds.

By 1994, the SMRU had established that the most effective strategy to control malaria in the refugee camps was to combine the early detection of cases with the treatment of all parasitaemic patients with a combination of mefloquine and artesunate. The Malaria Task Force was established to assist the medical NGOs working in the camps to utilize these results.