Men and women differ not only in their physical attributes and reproductive functions but also in many other characteristics, including the risks for some diseases as well as response to certain therapeutic treatments. Though genetically-identical for autosomal chromosomes, males and females could have gender-specific transcriptional or translational regulation, leading to differential mRNAs or protein products for some genes. To illustrate the gender-specific differences in mRNA-level expression, we compared gene expression patterns between males and females using a whole-genome microarray dataset on the unrelated HapMap lymphoblastoid cell lines derived from individuals of European (58 individuals) and African (59 individuals) ancestry. We applied the Gene Set Enrichment Analysis to identify any overrepresented predefined gene sets in either men or women. Distinct patterns of upregulation and downregulation of certain chromoSomal regions and other gene sets such as targets for certain microRNAs and transcription factors were identified in males or females, suggesting their potential roles in defining the gender-specific phenotypes. Gender-specific patterns of gene expression also appeared to be different between these two populations.