Common variable immunodeficiency (CVID) is a highly heterogeneous disease with an unpredictable pattern. CVID appears to have an immunologic and clinical phenotype similar to some hereditary humoral immunodeficiencies, including X-linked lymphoproliferative disease (XLP). The differential diagnosis of CVID and XLP is clinically of importance, because the two diseases have markedly different prognoses and treatment. The recent identification of the XLP gene, known as SH2D1A, has permitted a definitive diagnosis of XLP. In this report, we describe a male patient with XLP who initially received a diagnosis of CVID and developed a fatal course. Using genetic analysis, we confirmed that the patient harbored the SH2D1A gene mutation. The results support the notion that the possibility of a SH2D1A gene mutation should be considered in hypogammaglobulinemic male patients before a diagnosis of CVID is made.