El Salvador’s Ministry of Health provides a system of Western-style care through local clinics, regional hospitals and health centres, most of which are located in urban areas. Two of the country’s 30 hospitals are specialized institutes: the Bloom hospital for children and the Maternity Hospital, located in San Salvador, provide specialized treatment. Private hospital care is also available. A national social security program funded by payroll contributions provides medical insurance that includes sickness and maternity benefits, workers’ compensation and disability pensions. However, the system is available only to employees in formal businesses. Others rely on government-subsidized facilities.

For most Salvadorans, the family doctor is an important caregiver. The doctor, like the priest and teacher, has a vital role in the well-being of community members. Doctors are seen as authority figures and consequently have a great deal of influence. Challenging a doctor's diagnosis is unthinkable. However, most practitioners do not oppose the use of household remedies; many of these treatments are used to complement the doctor's own approaches.

Although health care has greatly improved in the past three decades, war, poverty ad natural disasters have hindered further improvements to El Salvador’s health care system and the populations’ overall health. Many people suffer from chronic malnutrition and illnesses linked to malnutrition and unsanitary living conditions, even though the average lifespan is 70 years. The country has a high infant mortality rate, and Salvadorans continue to die from preventable diseases such as measles. In cities, open sewage is a constant health threat. Piles of refuse get washed into the drinking water system each year during the rainy season, leading to a prevalence of dysentery and diarrhea, or mal de mayo. While not a serious threat to healthy people, mal de mayo is the leading cause of death in children under age five. The country continues to experience outbreaks of cholera, a deadly disease caused by impure drinking water. Various non-governmental organizations have been working for years to supplement the health care system and provide relief to those in most need.

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Some Salvadorans seek the advice of curanderos, who practice the Indian tradition of brujería (natural healing) and are believed to possess mystical powers. Curanderos may perform rituals or prescribe natural remedies of spices and herbal teas.