Background: Hypohidrotic ectodermal dysplasia (HED) is a group of disorders of ectodermal tissues, resulting from mutations in the ectodysplasin-A (EDA) pathway. Hypomorphic mutations in the NF-?B essential modulator (NEMO) result in HED with immunodeficiency (HED-ID, OMIM 300291), characterized by susceptibility to encapsulated bacteria, mycobacteria, and herpes virus infections. Objective: To analyze B-cell compartment and TLR9 signaling in HED-ID patients. Methods: Two HED-ID patients and a patient with HED caused by EDA gene mutation (XLHED) to confirm the implication of NFkB in this pathway were studied. Results: In HED-ID, differently from XLHED, only few B cells acquired the phenotype of IgM memory and differentiated into plasma cells upon TLR9 stimulation. Memory B cells did not produce IgG and IgA, and only small amounts of IgM in vitro. Conclusion: In HED-ID patients, TLR9 signaling is abnormal, in keeping with the lack of IgM memory B cells and natural antibodies. In individuals at a high risk of developing pneumococcal diseases, increased susceptibility to Streptococcus pneumonia infections and poor response to polysaccharide antigens have been associated with the lack of IgM memory B cells, required for the T-independent response toward encapsulated bacteria, whose differentiation from transitional B cells is under TLR9 control. This finding helps explain the susceptibility to infections by encapsulated bacteria.