Common variable immunodeficiency (CVID) is the most frequently diagnosed symptomatic primary immunodeficiency. CVID develops as a consequence of absence or malfunction of proteins involved with immunoglobulin production by plasma and memory B-cells. The last decade has brought us clarification of several genetic predispositions to the development of CVID. Despite considerable effort, however, for eighty-five percent of CVID patients, disease etiology remains undefined. We propose that in subsets of patients, CVID may involve defective assembly of protein complexes, which is crucial for example for B cell activation upon antigen triggering of the B cell receptor/co-receptor complex. Such defective protein-protein interactions may not be uncovered by standard gene sequencing methods, and may involve epigenetic or post-transcriptional regulation. In this review, we summarize recent developments in CVID research and propose additional approaches to the clarification of etiology of CVID patient groups, necessary for development of tailored treatment options.