In 1993, the government of Burkina Faso took on the project of improving the quality of health services by upgrading facilities and skills, achieving control of endemic parasitic diseases, and strengthening sector institutions. Total health care expenditures as of 1999 were an estimated 4.1% of GDP.
As of 1999, it was estimated that there were fewer than 0.05 physicians and 1.4 hospital beds per 1,000 people. The hospital at Ouagadougou is one of the most modern in Africa. Medical centers at Bobo-Dioulasso carry on research on insect-borne diseases. Mobile medical units attempt to control leprosy, sleeping sickness, yellow fever, and other contagious diseases. There were 2,824 new cases of measles in 1994.
One of Burkina Faso's most serious health problems is onchocerciasis (river blindness), which touches 84% of the total land area and causes many thousands of people to desert settlements infected by the fly vector. A control program has had some success. About two-thirds of Burkina Faso residents have access to safe water. In early 1997, a meningitis epidemic in West Africa spread to Burkina Faso, resulting in 724 deaths out of 5,571 cases.
The infant mortality rate in 2000 was 104 per 1,000 live births. The crude birth rate was 44.34 in 1999. The incidence of low-birth weight babies was 21% in 1993–96. As of 2000, only 12% of married women (ages 15 to 49) used contraception. As of 1999, Burkina Faso immunized children up to one year old as follows: diphtheria, pertussis, and tetanus, 42% and measles, 53%.
In 1999, there were 319 cases of tuberculosis per 100,000 people. Average life expectancy in 2000 was estimated at 44 years and the death rate was 17.1 per 1,000. At the end of 2001, the number of people living with HIV/AIDS was estimated at 440,000 (including 6.5% of the adult population) and deaths from AIDS that year were estimated at 44,000. HIV prevalence in 1999 was 6.44 per 100 adults.
In Burkina Faso, 70% of all women undergo female genital mutation. In 1994, 3.5 million women and girls were affected. Currently, no laws restrict this procedure.