**Abstract**

Primary Immunodeficiencies (PIDs) compose of a large spectrum of diseases characterized by abrogated or dysregulated functions of innate and adaptive immune system components that cause susceptibility to recurrent infections, autoimmunity, neoplasia/malignancy and dysfunction of organs and skeletal system. PIDs are also evaluated as molecular diseases due to the mutations in one or more genes. That affects transcripts and protein expressions as well as their functions. Today, 430 different genes are known to have various functional effects which are related to 403 different PIDs. Analyzing the effects of the mutations on relevant protein expression and function is significant to diagnose and the follow-up of the PIDs. Application of flow cytometry for analyzing protein expression levels and functions in immune cells as well as investigating the cellular functions tender a rapid, quantitative and reliable approach to identify and to prove the genetic background of PIDs. Therefore, the use of flow cytometry aids to have a large spectrum of data from gene to function and from function to clinical relevance in the first-step and differantial diagnosis of PIDs.

**Keywords:** Primary immunodeficiency, flow cytometry, molecular diagnosis, immunophenotyping, PBMC culture, functional assays, intracellular staining, PI3K pathway analysis- flow, CFSE cell proliferation
