AbstractX‐linked inhibitor of apoptosis (XIAP) deficiency is an infrequent inborn error of immunity caused by mutations in XIAP gene. Most cases present with absence of XIAP protein which can be detected by flow cytometry (FC), representing a rapid diagnostic method. However, since some genetic defects may not preclude protein expression, it is important to include a complementary functional test in the laboratory workup of these patients. L‐selectin (CD62‐L) is a molecule that is cleaved from the surface membrane of leukocytes upon stimulation of different receptors such as toll like receptors (TLRs) and nucleotide‐binding oligomerization domain‐like receptors (NLRs), including NOD2. Considering that XIAP deficiency impairs NOD2 signaling, we decided to assess CD62‐L down‐regulation by FC post‐stimulation of neutrophils and monocytes with L18‐muramyl Di‐Peptide (L18‐MDP), a NOD2 specific agonist, in order to develop a novel assay for the functional evaluation of patients with suspicion of XIAP defects. Whole blood samples from 20 healthy controls (HC) and four patients with confirmed molecular diagnosis of XIAP deficiency were stimulated with 200 ng/mL of L18‐MDP for 2 h. Stimulation with 100 ng/mL of lipopolysaccharide (LPS) was carried out in parallel as a positive control of CD62‐L shedding. CD62‐L expression was evaluated by FC using an anti CD62‐L‐ antibody and down‐regulation was assessed by calculating the difference in CD62‐L expression before and after stimulation, both in terms of percentage of CD62‐L expressing cells (Δ%CD62‐L) and median fluorescence intensity (ΔMFI%). Neutrophils and monocytes from XIAP deficient patients displayed a significantly diminished response to L18‐MDP stimulation compared with HC (p < 0.0001), indicating a severely altered mechanism of CD62‐L down‐regulation following activation of NOD2‐XIAP axis. On the other hand, the response to LPS stimulation was comparable between patients and heathy controls, suggesting preserved CD62‐L shedding with a different stimulus. FC detection of CD62‐L down‐regulation in monocytes and neutrophils after whole blood stimulation with L18‐MDP results in an effective and rapid functional test for the identification of XIAP deficient patients.