Hyper-immunoglobulin E (IgE) syndrome (HIES) is one of the primary immunodeficiency syndromes. Although the cytokine dysregulation is suggested to play a role in its pathophysiology, the causative gene has not yet been identified. To investigate the pathophysiology and candidate genes involved in this disease, we performed microarray analysis of unstimulated peripheral CD4+ T cells and CD14+ cells, as well as peripheral blood mononuclear cells (PBMNC) stimulated with Staphylococcus aureus isolated from HIES patients and healthy controls. By microarray analysis, 38 genes showed over 2-fold differences between the HIES patients and healthy controls in purified CD14+ cells, although only small differences in the gene expression profiles were observed between the two groups in purified CD4+ T cells. RGC32 expression levels showed the greatest difference between the two groups, and were significantly elevated in HIES compared with those in severe atopic dermatitis or healthy controls using real-time PCR. A significantly larger number of lysosome-related genes were up-regulated, and significantly larger number of genes related to cell growth and maintenance were down-regulated in HIES. After the stimulation of PBMNC with Staphylococcus aureus, 51 genes showed over 3-fold differences between HIES patients and healthy controls. A significantly large number of immunoglobulin-related genes were up-regulated in HIES. The distinct patterns of gene expression profiles and RGC32 expression levels will be useful for understanding the pathophysiology and for diagnosis of HIES, respectively.