The Men1 gene has been identified as the gene responsible for MEN1, a hereditary syndrome transmitted with an autosomal dominant trait. Disruption of the Men1 gene results in defects of multiple organs development, including the nervous system, heart, liver, cranium, and face. In this study, we used embryoid bodies (EBs) formed from wild-type and Men1−/− ES cells as a model system to investigate effect of Men1 gene on the embryo development. We characterized in detail gene expression profile of these Men1−/− EBs by microarray techniques and identified a series of putative menin targeted genes, including genes involved in development of bone (e.g., Postn, Runx2, and Msx2), liver (e.g., KDR), blood (e.g., Hox9 and Kitl), and pancreatic islet (e.g., Sox4, Foxa1, Btc, Igf2, and Nfatc1). Further studies may shed light onto the underlying mechanisms of the interplay between menin and these genes.