Mendelian susceptibility to mycobacterial disease (MSMD) is a rare syndrome conferring predisposition to clinical disease caused by weakly virulent mycobacteria, such as Mycobacterium bovis Bacille Calmette Guérin (BCG) vaccines and nontuberculous, environmental mycobacteria (EM). Since 1996, MSMD‐causing mutations have been found in six autosomal genes involved in IL‐12/23–dependent, IFN‐γ–mediated immunity. The aim of this review is to provide the description of the two described forms of X‐linked recessive (XR) MSMD. Germline mutations in two genes, NEMO and CYBB, have long been known to cause other human diseases—incontinentia pigmenti (IP) and anhidrotic ectodermal dysplasia with immunodeficiency (EDA‐ID) (NEMO/IKKG), and X‐linked chronic granulomatous disease (CGD) (CYBB)—but specific mutations in either of these two genes have recently been shown to cause XR‐MSMD. NEMO is an essential component of several NF‐κB–dependent signaling pathways. The MSMD‐causing mutations in NEMO selectively affect the CD40‐dependent induction of IL‐12 in mononuclear cells. CYBB encodes gp91phox, which is an essential component of the NADPH oxidase in phagocytes. The MSMD‐causing mutation in CYBB selectively affects the respiratory burst in macrophages. Mutations in NEMO and CYBB may therefore cause MSMD by selectively exerting their deleterious impact on a single signaling pathway (CD40–IL‐12, NEMO) or a single cell type (macrophages, CYBB). These experiments of Nature illustrate how specific germline mutations in pleiotropic genes can dissociate signaling pathways or cell lineages, thereby resulting in surprisingly narrow clinical phenotypes.