In Indonesia, only antimalarials chloroquine, sulfadoxine/ sulfalene-pyrimethamine, quinine, and primaquine are available. The development of chloroquine and multidrug resistance poses a therapeutic challenge. In order to obtain alternative antimalarial drugs, trials were conducted of malaria treatment and prophylaxis in several chloroquine or multidrug resistance areas. The objective of these trials was to assess the efficacy and safety of the alternative antimalarial drugs. All the trials were mostly open studies in the fields and hospitals. These were collaboration studies between Communicable Disease Research Center, Communicable Disease Control and Environmental Health, Faculty of Medicine of the University of Indonesia, NAMRU-2, and local health staff. The patients were selected according to the WHO criteria for in-vivo antimalarial drug sensitivity testing. They should sign the informed consent form and they were followed up during the study, for 2 weeks - 4 months. In chloroquine and multidrug resistance areas, mefloquine, halofantrine, and artemether are effective and safe for treatment of uncomplicated falciparum malaria. While artesunate was noted effective and safe only in the first 14 days. Halofantrine was also documented effective and safe for vivax malaria treatment. Intramuscular artemether was effective and safe for treatment of severe and complicated falciparum malaria, particularly in remote areas lacking hospitals and the capability for intravenous infusion. Primaquine, doxycycline and mefloquine are effective and safe for malaria prophylaxis. Since the new antimalarials are not yet available in Indonesia, the improvement of efficacy of antimalarial drugs currently available should be studied. Prophylactic drugs which are effective and safe for children, pregnant and lactating women should also be studied.