Human exhibit sexual dimorphism early in development and throughout life. Here we stringently analyzed gene expression in inbred non-human primate embryonic stem cells (nhpESCs) searching for sexually dimorphisms. We utilized location-specific probes solely, thus avoiding probe cross-reactivity between members of gene families and genomic gene duplications. Seventeen sexually dimorphic transcripts (15 genes, out of which 9 autosomals) were identified, of which five were verified using real-time q-PCR. We compared these results from pedigreed nhpESCs with available human ESCs datasets. Three human X-linked genes show sexual dimorphism. Thus, these results enhance our knowledge and deepen our understanding on early development processes for sexual dimorphism. (C) 2011 Elsevier Inc. All rights reserved.