Flow cytometry, as a useful technology, has played an important role in the progress in basic and clinical research by measuring multiple char-acteristics of individual cells in a high-throughput manner. One of the most important applications of flow cytometry is the initial workup and subse-quent management of inborn errors of immunity (IEI). IEIs, also known as primary immunodefi-ciencies, are a heterogeneous group of inherited disorders of immune system, presenting with heterogeneous clinical manifestations. Given that IEI patients present heterogeneous clinical and immunological features, diagnosing IEI using only clinical and conventional laboratory data is challenging. Genetic tests, including whole exome sequencing (WES) and whole genome sequenc-ing (WGS), are involved in the identification of genetic defects in IEI; however, flow cytometry remains an important first step in defining the immunophenotype of the patient prior to genet-ic analysis. The applications of flow cytometry in the evaluation of IEI are diverse and include identifying distinct populations of immune cells, quantifying the expression of intracellular and intranuclear proteins, functionally validating ge-netic variants, monitoring treatment, defining the genotype-phenotype correlation, detecting carri-ers, and classifying disorders.