Selective IgM deficiency (SIgMD) is a rare primary immunodeficiency disease, which is found in some patients with autoimmune diseases. The pathogenesis of SIgMD and the relationship of these diseases have remained unclear. The absence of secreted IgM was recently reported to accelerate the development of autoimmune diseases in lupus-prone lymphoproliferative (Ipr) mice. The reduction of secreted IgM production may relate with the progression of autoimmune diseases in human. We present a case of SIgMD associated with systemic lupus erythematosus (SLE), and examined the function and the IgM heavy chain gene of patient's lymphocytes. The number and the surface IgM expression of the patient's B cells were normal. In vitro stimulation of peripheral mononuclear cells by recombinant IL-2 and a B cell activator, Staphylococcus aureus Cowan strain I, could not overcome the reduction of IgM production, although the secreted form of IgM mRNA was detected. Sequence analysis of the IgM heavy chain gene and the IgM mRNA revealed no mutation or deletion. These findings suggested that SIgMD in this case was involved in the abnormality during B cell maturation. Further analysis is required to reveal the pathogenesis of SIgMD associated with SLE.