Human peripheral blood is a useful material for biomedical research, since it can be used to investigate responses to treatment and predict diseases. However, various biological and technological factors produce a large degree of variation in blood of gene expression profiles. Our study was based on gene expression profiling analysis on peripheral blood of 45 healthy volunteers, 21 females and 24 men. The blood cells were concentrated, and the total RNA was isolated for the analysis of gene expression using the Affymetrix Gene Chip technology. The results were obtained by a fluorescent scanner, and the numerical data was analyzed using Bioconductor. Samples were clearly divided by gender through the unsupervised clustering analysis. 40 identified genes, differentiating samples by gender were analyzed according to their biological function and chromosomal location. Most of them are located on the X and Y chromosomes. These results provide new insights into the genetic makeup which distinguishes both sexes probably associated with diseases and sex determination.