Malaria is still a health problem in the world, particularly in Indonesia with high morbidity and mortality rate. Increased mortality rate due to malaria has been reported and it may occur because of the raising in anti-malarial resistance. Chloroquine-resistant P. vivax and P. falciparum have been reported in almost all over the country. Various dose administrations of anti-malarial treatment, instead of the standard dose and single dose treatment is probably one of possible causes. Another problem in Indonesia includes the shortage in diagnostic facilities as well as various kinds of treatment available. In 2009, Ministry of Health, Republic of Indonesia has declared the program of Malaria Elimination 2009 to overcome the problems. The policy includes diagnosis and treatment of malaria. It is expected that diagnosis should be established based on the gold standard by confirmation of blood smears. Moreover, first line treatment of malaria shall include the Artemisinin Combination Therapy (ACT). Artemisinin is selected as it has some advantages and it should be combined to prevent resistance. Principles of severe malaria management are preventing and minimizing the risk of death. Adequate treatment includes supportive and causal (anti-malarial) treatment as well as treating complication. Parenteral artemisinin is given for severe malaria and continued with oral combination of artemisinin treatment once the patient can take oral therapy.