Primary immunodeficiency diseases (PID) provide invaluable insight into immune system, notably in vivo immune responses to microorganisms as based on the variable vulnerability to pathogens and opportunistic agents. PID are also very informative in defining key checkpoints controlling immunity to self. Despite a Mendelian inheritance of most PID, mutations of a given gene can lead to a vast array of phenotypes as a function of the type of mutations, environmental factors, the occurrence of additional somatic mutations, or regulatory factors, which add considerable but hitherto underestimated complexity. Understanding the molecular pathophysiology of PID is not only contributing to a better knowledge of the immune system but may also favor new therapeutic approaches.