Somalia has a high incidence of tuberculosis (an estimated 365 cases per 100,000 people in 1999), schistosomiasis, and pulmonary disturbances. Malaria and intestinal parasites are endemic. Serious dietary deficiencies are found, particularly in the north. In 1990–96, only 31% of the population had access to pure drinking water, which is rarely available outside the larger cities. Water outside these centers needs to be filtered, boiled, or chemically treated. Somalis, however, take few of these precautions. A very low 17% of the population had adequate sanitation in 1990-96, and only 27% had access to health care services.

Immunization rates for children up to one year old in 1990–95 were: tuberculosis, 31%; diphtheria, pertussis, and tetanus, 18%; polio, 18%; and measles, 30%. The rates for DPT and measles as of 1999 were, respectively, 18% and 26%. The number of AIDS cases in 1995 was low, with only 13 cases reported in that year. As of 2001, there were an estimated 43,000 people living with HIV/AIDS. In 1994, there were 2,023 tuberculosis cases. The previous year 3,049 malaria cases had been reported.