Although medical treatment in government hospitals and dispensaries is free, facilities deteriorated greatly under Amin's rule. Following the 1978–79 war of liberation, many hospitals were left without medicine or beds. A new government health care policy in 1993 outlined goals for restoration of a cohesive network of health care services. As of 2000, however, Uganda's health indicators were still poor, even in comparison with those of other African countries. Containment of serious diseases, such as cholera, dysentery, tuberculosis, malaria, schistosomiasis, sleeping sickness, typhus, and leprosy, has been made difficult by poor sanitation and unclean water. Other barriers to health care access for the rural poor were distance from providers, cost of services, and inadequate quality of health care. Less than half the population lives within 5 km (3 mi) of a health care facility. An estimated 71% of the population had access to health care services in 1994. The most serious obstacle to health has arisen from nutritional deficiencies, particularly among children. The goiter rate was 75 per 100 school-age children in 1996. Malaria remains the country's most serious health threat, even more so than AIDS. In 2000, 50% of the population had access to safe drinking water and 75% had adequate sanitation. As of 1999, it was estimated that there were fewer than 0.05 physicians per 1,000 people, and 0.9 hospital beds. As of 1999 total health care expenditure was estimated at 5.9% of GDP.
Planned health care projects in the 1990s included: rehabilitation of buildings, equipment, fittings, and services; institutional support and training; designs for five district hospitals and 10 rural centers; and a mental health rehabilitation study. Venereal disease continues to be a problem in the adult population and AIDS became a severe problem in the 1980s, with an estimated 800,000 Ugandans HIV-positive in 1989. The country plans to focus on health care awareness and education—in particular, family planning and AIDS. Prevention strategies that change high-risk sexual behavior have had a direct impact on HIV infection rates in Uganda. At the end of 2001, the number of people living with HIV/AIDS was estimated at 600,000 (including 5% of the adult population) and deaths from AIDS that year were estimated at 84,000. HIV prevalence in 1999 was 8.3 per 100 adults.
The life expectancy was only 42 years in 2000 and the fertility rate was 6.2. Only 15% of married women ages 15–44 used any form of contraception as of 2000. As of 2002, the crude birth rate and overall mortality rate were estimated at, respectively, 47.2 and 17.5 per 1,000 people. Immunization rates for 1997 for children up to one year old were high: tuberculosis, 84%; diphtheria, pertussis, and tetanus, 58%; polio, 59%; and measles, 60%. Commonly reported diseases were guinea worm (4,810 cases in 1995 versus 43,000 in 1991), measles (42,659 cases in 1995), and tuberculosis, (14,763 cases in 1994). In 1999, there were 343 cases of tuberculosis per 100,000 people.