Common variable immunodeficiency (CVID) is a disease characterized by increased susceptibility to infections, hypogammaglobulinemia and immune dysregulation. Although CVID is thought to be a disorder of the peripheral B-cell compartment, in 25% of patients early B-cell development in the bone marrow is impaired. As poor B-cell reconstitution after hematopoietic stem cell transplantation has been observed, we hypothesized that in some patients the bone marrow environment is not permissive to B-cell development. Studying the differentiation dynamics of bone marrow-derived CD34+ cells into immature B-cells in vitro allowed us to distinguish patients with B-cell intrinsic defects and patients with a non-permissive bone marrow environment. In the former immature B-cells did not develop and in the latter CD34+cells differentiated into immature cells in vitro, but less efficiently in vivo. In a further group of patients, the uncommitted precursors were unable to support the constant development of B-cells in vitro, indicating a possible low frequency or exhaustion of the precursor population. Hematopoietic stem cell transplantation would result in normal B-cell repopulation in case of intrinsic B-cell defect, but in defective B-cell repopulation in a non-permissive environment. Our study points to the importance of the bone marrow niche in the pathogenesis of CVID.