Selective IgE deficiency (IgED) is currently defined as a significant decrease in serum levels of IgE (<2 kIU/L) in a patient whose other immunoglobulin levels are normal. There are no published large-scale epidemiological studies regarding the prevalence of and clinical features of IgED. In the population-based case-control study, we investigated clinical and laboratory characteristics of patients with IgED. Case samples were drawn from all subjects (n = 18487), with serum total IgE measurement during 2012 at Leumit Health Care Services (Israel) and had serum total IgE of <2 kIU/L. The control group was randomly sampled from the remaining 18,261 subjects with a case-control ratio of four controls for each case (1:4). Comorbid diseases were identified by specific International Classification of Diseases, Ninth Revision, Clinical Modification diagnostic codes given by the corresponding board-certificated physicians. Two hundred twenty-six subjects showed serum total IgE levels of <2 kIU/L; 68 (30.9%) were between the ages of 4 and 12 years (children) and 250 (69.1%) were ≥12 years old (adults). Matched control groups were selected for each age group. The children group was characterized by higher prevalence of asthma and hyperreactive airways disease; and both children and adult groups had significantly higher prevalence of chronic sinusitis, otitis media, autoimmune, and oncological diseases than their respective controls. Undetectable serum total IgE may serve as a marker of immune dysregulation and autoimmunity.