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Located in southeast Asia, East Timor was a Portuguese colony from 1702, and in 1951 became an overseas province of Portugal. In August 1975, there was a civil war, and soon afterward, Indonesia invaded East Timor, occupying it until 1999 when it was controlled by the United Nations. In May 2002, it finally gained independence.

During most of the period of Portuguese rule, the healthcare services were underdeveloped. Many of the health problems in East Timor were because of malaria and other insect-borne diseases, as well as poor hygiene. To improve these, J. Gomes da Silva was appointed to take over the running of medical services in East Timor, and found that the hospital was badly equipped, and all the Christian cemeteries were badly positioned, causing possible contamination of the water supply for Dili and other towns, and being a probable source of cholera. No action was taken on the report he made on the problems he found. In December 1940, José dos Santos Carvalho was appointed as the health delegate for the central and eastern parts of East Timor, remaining there during the Japanese Occupation, and writing the major work on the history of medicine in East Timor.

In 1948, there were four hospitals and six doctors in East Timor. The health problems at the time included malaria, pneumonia, elephantiasis, tuberculosis, cholera, and venereal diseases. Four years later, in 1952, the First National Congress of Tropical Medicine was held in the Portuguese capital, Lisbon. Annual congresses were held for the next few years where Portuguese colonial administrators coordinated their medical care programs, which at that stage were mainly for the Portuguese and other Europeans. By 1958, the congresses had become renamed the International Congress for Tropical Medicine and Malaria, and over the next few years the World Health Organization led campaigns to eradicate malaria which did affect many people in East Timor.

When Indonesia invaded East Timor in 1975, there was only one major hospital, located in Dili, the administrative capital of East Timor. Even though the vast majority of the population of East Timor opposed the Indonesian Occupation, many did accept that the Indonesians did massively improve healthcare in what became their 27th province. Indeed, prior to the Indonesian invasion, there was only one surgeon and one dentist covering the entire population of 610,000, although there were often a dozen doctors serving in the Portuguese army. From 1976 until 1999, the provision of healthcare in East Timor was much better than many other parts of Indonesia, with the Indonesian government eager to win over the population of the place. More hospitals were built, and clinics opened in many small towns. However, in 1999, in a referendum, the people voted heavily in favor of independence. After this, pro-Indonesian militia destroyed much of the government infrastructure in the place. This destruction saw the burning down of clinics and medical centers around the country.

Since 1999, there have been attempts to rebuild the East Timorese health services, and the presence of large numbers of United Nations and foreign soldiers and officials in the country, several hospitals were refurbished. Malaria still remains a major problem in the country, with problems over dengue fever, tuberculosis, and cholera.

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