Sex hormones are likely to be involved in sex differences in adipose tissue distribution. To test whether estrogen regulates genes expressed in the adipose tissue in a site-specific manner, we studied the effect of exogenous estradiol on the gene expression in visceral and subcutaneous adipose tissues of male ob/ob mice. We screened genes expressed in a site- and sex-specific manner, and genes that were affected by exogenous estradiol by DNA chip analysis. They were verified by real-time PCR. Myosin heavy chain 2B (Myh4) and phosphoglycerate mutase muscle-specific subunit (Pgam) were expressed specifically in the subcutaneous adipose tissue, and uroplakin IIIb (UP3) was expressed specifically in the visceral adipose tissue. DEAD-box Y RNA helicase (DBY) and eukaryotic initiation factor 2 gamma Y (eIF2gamma Y) were expressed only in male adipose tissue. X-chromosome inactive specific transcript (Xist) was expressed only in female adipose tissue. When estradiol was subcutaneously administrated to male mice, the expression of monocyte-chemoattractant protein-1 (MCP-1) and androgen receptor (AR) genes was regulated in a site-specific manner. The difference in the amount of estrogen receptor did not account for the site-specific effect of estrogen. Our findings show that estrogen affects the expression of some adipocyte genes in a site-specific manner.