The collapse of the government in January 1991 with the fall of Siad Barre led to further deterioration of Somalia's health situation. The high incidence of disease that persisted into the early 1990s reflected a difficult environment, inadequate nutrition, and insufficient medical care. In the years since the revolutionary regime had come to power, drought, flood, warfare (and the refugee problem resulting from the latter) had, if anything, left diets more inadequate than before. Massive changes that would make the environment less hostile, such as the elimination of disease-transmitting organisms, had yet to take place. The numbers of medical personnel and health facilities had increased, but they did not meet Somali needs in the early 1990s and seemed unlikely to do so for some time.

The major maladies prevalent in Somalia included pulmonary tuberculosis, malaria, and infectious and parasitic diseases. In addition, schistosomiasis (bilharzia), tetanus, venereal disease (especially in the port towns), leprosy, and a variety of skin and eye ailments severely impaired health and productivity. As elsewhere, smallpox had been virtually wiped out, but occasional epidemics of measles could have devastating effects. In early 1992, Somalia had a human immunovirus (HIV) incidence of less than 1 percent of its population.

Environmental, economic, and social conditions were conducive to a high incidence of tuberculosis among young males who grazed camels under severe conditions and transmitted the disease in their nomadic wanderings. Efforts to deal with tuberculosis had some success in urban centers, but control measures were difficult to apply to the nomadic and seminomadic population.

Malaria was prevalent in the southern regions, particularly those traversed by the country's two major rivers. By the mid1970s , a malaria eradication program had been extended from Mogadishu to other regions; good results were then reported, but there were no useful statistics for the early 1990s.

Approximately 75 percent of the population was affected by one or more kinds of intestinal parasites; this problem would persist as long as contaminated water sources were used and the way of life of most rural Somalis remained unchanged. Schistosomiasis was particularly prevalent in the marshy and irrigated areas along the rivers in the south. Parasites contributed to general debilitation and made the population susceptible to other diseases.

Underlying Somali susceptibility to disease was widespread malnutrition, exacerbated from time to time by drought and since the late 1970s by the refugee burden. Although reliable statistics were not available, the high child mortality rate was attributed to inadequate nutrition.

Until the collapse of the national government in 1991, the organization and administration of health services were the responsibility of the Ministry of Health, although regional medical officers had some authority. The Siad Barre regime had ended private medical practice in 1972, but in the late 1980s private practice returned as Somalis became dissatisfied with the quality of government health care.

From 1973 to 1978, there was a substantial increase in the number of physicians, and a far greater proportion of them were Somalis. Of 198 physicians in 1978, a total of 118 were Somalis, whereas only 37 of 96 had been Somalis in 1973.

In the 1970s, an effort was made to increase the number of other health personnel and to foster the construction of health facilities. To that end, two nursing schools opened and several other health-related educational programs were instituted. Of equal importance was the countrywide distribution of medical personnel and facilities. In the early 1970s, most personnel and facilities were concentrated in Mogadishu and a few other towns. The situation had improved somewhat by the late 1970s, but the distribution of health care remained unsatisfactory.