Background: Common variable immunodeficiency (CVID) is the most frequent symptomatic primary immunodeficiency, which manifests a wide range of clinical phenotypes from recurrent infections of the respiratory system to autoimmunity, enteropathy and lymphoproliferative disorders. Some abnormalities in T and B lymphocyte subpopulations may associate with the development of such clinical complications. Aim of study: The main objective of this case-control study is to investigate the frequency and absolute count of different lymphocyte subsets in CVID patients as well as the cellular proliferation response. Correlation between lymphocyte abnormalities and different clinical phenotypes of the disease such as infection only (IO), autoimmunity (AI), chronic enteropathy (CE) and lymphoproliferative disorders (LP) are determined. We also aim to evaluate the prognosis of CVID for each clinical manifestation based on lymphocyte phenotype. Methods: A population of genetically unsolved CVID patients after whole exome sequencing (WES) will be subdivided into 4 clinical phenotypes i.e. IO, AI, CE and LP and an equal number of age and sex-matched healthy controls (HC) will be examined for the frequency of distinct subgroups of CD19+ B cells, CD4+ T cells and CD8+ T cells by flow cytometry. The proliferation response of their CD4+ T cells is then evaluated by Carboxyfluorescein succinimidyl ester (CFSE) test, using stimulation of isolated peripheral blood mononuclear cells with anti-CD3 and anti-CD28 antibodies. Data analysis will be assessed by parametric or nonparametric tests based on normality of data distribution using IBM SPSS Statistics, V.24 and Stata software V.14. Ethics and dissemination: Ethical approval of this study is received from the Ethics Committee of Tehran University of Medical Sciences (ID number: IR.TUMS.VCR.REC.1396.3380) and all participants will be asked to sign the informed consent statement. Due to the wide range of variables, objectives and questions, the findings of this study are intended to release as multiple publications in peer-reviewed journals and presented at national and international conferences.