•BPA and NP affect the expression of pre- and early-meiotic germ cell marker genes.•GO-based microarray analysis using published GeneChip data identified the functions of EDCs.•BPA and NP affect genes with GO terms related to germ cell development and reproduction.•Feminizing effect of BPA and NP might be attributed to the suppression of male gonadal development. Effects of endocrine disrupting chemicals (EDCs) on reproduction have not been fully explained comprehensively. In this study, we tried to validate the common effect of Bisphenol A (BPA) and Nonylphenol (NP) on the differentiation of embryonic stem (ES) cells and found that they modify the expression of germ cell specific genes. To elucidate functional significance on biological process, we performed Gene Ontology (GO)-based microarray analysis comparing with published GeneChip data of primordial germ cell development in vivo. Cluster analysis of gene expression profile revealed that EDC treatment and primordial germ cell (PGC) development shared characteristic cluster consists of GO terms related to “germ cell development” and “reproduction”. In the GO term “reproduction”, meiosis related genes showed high expression level by EDC exposure. These results suggest that BPA and NP affect not only some of the germ cell specific genes, but functionally interferes germ cell development and reproduction.