Establishing the definitive diagnosis in the case of inherited immune defects (IID) is often challenging because the clinical features can be heterogeneous, atypical and overlapping different disease entities. The next generation sequencing technology (NGS) allows identifying genetic variants that are responsible for the observed clinical presentations. The use of NGS applied to the genes mutated in IIDs or known to be involved in the development, differentiation and regulation of the immune system allows to target hundreds of relevant genes in well characterized patients suspected of carrying inherited immune defects. This approach answers both diagnostic and research needs, facilitates the understanding of the mechanisms that underlie IIDs, and ultimately leads to the discovery of new therapeutic targets.