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Adipose tissue (AT) located in the viscera is considered to be functionally and metabolically different from that found in the subcutaneous depot. However, subcutaneous AT (SAT) in generalized regions is considered to be homogeneous in nature. Affymetrix GeneChip Human Exon 1.0 ST Arrays were used to determine differential gene expression in four subcutaneous adipose depots (upper abdomen, lower abdomen, flank and hip) in normal weight women. A total of 2,890/24,409 transcripts were differentially expressed between all sites. When comparing the hip and flank to the lower abdomen, 248 and 83 genes were differentially expressed, respectively. When comparing the hip and flank to the upper abdomen, 2,480 and 79 genes were differentially expressed, respectively. No genes were significantly different when the lower abdomen was compared to the upper abdomen and the hip to the flank. Genes involved in the complement and coagulation cascades and immune responses showed increased expression in the lower abdomen compared to the flank. In addition, two genes involved in the complement and coagulation cascade, CR1 and C7, were expressed more highly in the lower abdomen compared to the hip. Genes involved in basic biochemical metabolism including insulin signaling, the urea cycle, glutamate metabolism, arginine and proline metabolism and aminosugar metabolism had higher expression in the lower abdomen compared to the hip. These results in normal weight healthy women provide a new perspective on regional differences in SAT biology that may have pathophysiologic implications when adiposity increases.