There are two subclasses of IgA, IgA1 and IgA2, and its heavy chains are encoded by two different genes, alpha1 and alpha2 genes. These two subclasses play important roles in the first line of defense, and the amount ratio of these molecules in secretions varies. IgA deficiency (IgAD) is the most common immunodeficiency, however the pathogenesis in most cases of IgAD is unknown. The class switch disorder in IgA producing B lymphocytes is one of the important factors in IgAD patients. The decreased expression levels of Ialpha germline transcripts before a class switch may be the cause of selective IgAD. The alpha1 and alpha2 gene expression levels are low in most IgAD patients. Using RT-PCR method in which alpha1 and alpha2 mRNAs can be separately evaluated, we identified the second case of alpha1 gene deletion in Japan. Longitudinal change in the serum IgA of the patient with alpha1 gene deletion showed the pattern of the partial IgAD. Patients with alpha1 gene deletion can be considered as having partial IgAD.