Approximately 100 individuals with eosinophil peroxidase deficiency have been described in the scientific literature. Based on blood test data, varying estimates of the prevalence of the condition have been reported in specific populations. Eosinophil peroxidase deficiency is estimated to occur in 8.6 in 1,000 Yemenite Jews, in 3 in 1,000 North-African Jews, and in 1 in 1,000 Iraqi Jews. In northeastern Italy, the condition occurs in approximately 1 in 14,000 individuals; in Japan it occurs in 1 in 36,000 people; and in Luxembourg, eosinophil peroxidase deficiency is thought to occur in 1 in 100,000 people.

Mutations in the EPX gene cause eosinophil peroxidase deficiency. The EPX gene provides instructions for making the eosinophil peroxidase protein. During an immune response, activated eosinophils release eosinophil peroxidase at the site of injury. This protein helps form molecules that are highly toxic to bacteria and parasites. These toxic molecules also play a role in regulating inflammation by fighting microbial invaders.

EPX gene mutations reduce or prevent eosinophil peroxidase production or result in a protein that is unstable and nonfunctional. As a result, eosinophils have severely reduced amounts of eosinophil peroxidase or none at all. Other proteins within affected eosinophils are normal, and while the cells lacking eosinophil peroxidase are smaller and may have structural changes, the loss of eosinophil peroxidase does not appear to impair the function of eosinophils.