A large number of health centers and hospitals were severely damaged or destroyed due to independence-related violence. The new nation also found itself lacking medical professionals, since the vast majority of health workers were Indonesian nationals who left the area. Post-independence, most health care has been provided by international NGOs under the general direction of the Division of Health Services (est. July 2000), which works in cooperation with the World Health Organization (WHO) to develop healthcare policies and coordinate services throughout the country.
In 2000, primary health care was provided by fifteen international NGOs, six local NGOs, twenty-three religious organizations, four military groups, and two private/business agencies. There were two hospitals operating in Dili and one in Baucau. In 2001, a program of District Health Plans included 64 community health centers, 88 health posts, and 117 mobile clinics. There is a laboratory in Dili. There were an estimated 2,000 health workers in the country, including 28 East Timorese doctors.
Though current figures are uncertain, estimates suggest that the 2002 life expectancy rate was 64.85 years (male, 62.64 years; female: 67.17 years). The same year, the fertility rate was estimated at 3.88 children born per woman. The birth rate was estimated at 28.07 births per 1,000 people. Infant mortality was estimated at 52 deaths per 1,000 live births, but this figure may be conservative since most births are not attended by skilled professionals. The most common causes of infant deaths have been infections, prematurity, and birth trauma. It was further estimated that 125 out of 1,000 children died before the age of five. In 2001, maternal mortality was estimated at 890 per 100,000 live births, with the most common cause of death being severe postpartum bleeding.
In 2000, the World Health Organization reported that about 3–4% of all children ages six months to five years were acutely malnourished and 20% were chronically malnourished. Intestinal parasitic infections affect about 80% of all children. Other common childhood illnesses include acute respiratory diseases, diarrheal conditions, malaria, and dengue fever. An immunization program was reinstated in March 2000, which included a special campaign that immunized 45,000 children against measles. In November and December 2000, a nationwide polio immunization campaign reached about 84% of the population.
Endemic diseases include malaria, leprosy, and lymphatic filiariasis. Tuberculosis is a major problem as well, affecting over 8,000 people as of 2000 (31% under the age of 15 years). Sexually transmitted diseases are prevalent. The major causes of death are communicable diseases (60%), noncommunicable diseases, chronic diseases, traffic accidents, and others.