Following independence, The World Health Organization (WHO) assisted in the organization of public health services and the training of sanitarians and public health nurses for Burundi. Students from Burundi received medical training at universities in France and in the Democratic Republic of the Congo. WHO coordinated all public health programs and helped in campaigns against smallpox, tuberculosis, and malaria. WHO, the UN Food and Agriculture Organization, and UNICEF also provided aid for nutrition and maternal and child health programs. Following the assassination of the president of Burundi in 1993, widespread violence involving tribal groups uprooted many of the country's people. Approximately 683,000 people fled to neighboring countries, rural villages, or towns where sanitation is poor.
Since January 1997, nearly 50,000 new cases of louse-born typhus have been reported, the largest outbreak to occur in 50 years. Outbreaks of group A meningitis are occurring in Burundi. There have been over 2,500 cases of meningitis. Trypanosomiasis (sleeping sickness), borne by the tsetse fly, is a problem in the Ruvuvu River Valley. Malaria and schistosomiasis (bilharziasis) are common along the Ruzizi River. Intake of animal protein and fat is inadequate and almost all diseases associated with malnutrition are found in Burundi. There was a cholera epidemic in 1978, due to insufficient sewage facilities. In 1995, 2,297 cases of cholera were reported. A four-year program covering 30–40% of the country, started in 1986, was intended to rehabilitate and expand rural water supplies. In 1994 and 1995, 58% of the population had access to safe water.
In 1990, there were 317 doctors, 55 pharmacists, and 9 dentists. As of 1999, there were an estimated 0.1 physicians and0.7 hospital beds per 1,000 people. Total health care expenditures as of 1999 were estimated at 3.7% of GDP.
In 2000, the infant mortality rate was 102 per 1,000 live births. The maternal mortality rate of 1,900 per 100,000 live births (according to 1995 estimates) was one of the highest in Africa. From 1980 to 1993, only 9% of married women (ages 15 to 49) practiced contraception. In 1999, Burundi immunized children up to one year of age as follows: diphtheria, pertussis, and tetanus, 74% and measles, 75%. In 1990, 38% of children under five years old were considered to be malnourished.
Average life expectancy in 2000 was estimated at 42 years. In 1999, there were 382 cases of tuberculosis per 100,000 people. There were approximately 8,000 war-related deaths during the conflict between the Tutsis and Hutus from 1988 to 1992. The death rate was estimated at 16 per 1,000 as of 2002. At the end of 2001, the number of people living with HIV/AIDS was estimated at 390,000 (including 8.3% of the adult population) and deaths from AIDS that year were estimated at 40,000. HIV prevalence in 1999 was 11.32 per 100 adults.