Objective To investigate the effects of menin, product of multiple endocrine neoplasia type 1 (Men1) gene, on related genes of early development of mouse embryos, and explore its possible mechanism. Methods Undifferentiated mouse embryonic stem cells were maintained on a feeder layer of Mitomycin C-treated mouse embryonic fibroblasts, and embryoid bodies (EBs) were formed after initiating differentiation. The expression of marker gene in embryonic development period of EBs was identified by RT-PCR. Chromosome immunoprecipitation and DNA microarray were conducted to detect the downstream genes regulated by menin in mouse EBs, and the results were identified by Real-Time PCR. Results It was revealed by RT-PCR that EBs corresponded to the early organogenesis stage of mouse embryonic development. In the microarray containing 8 640 oligonucleotides representing about 8 000 genes in the genome, 784 genes were identified as downstream. These genes were then classified into cellular signaling pathways and were identified, including Wnt signaling pathways (1500003O03Rik, Prkca, Fosl1, Nfatc3 and Dvl1), MAPK signaling pathways (Casp6, Arrb2, Fgf15, 1500003O03Rik, Map3k4, Map2k1ip1, Tgfb3, Prkca, Traf2, Dusp7 and Atf2), TGF-β signaling pathways (Thbs1, Tgfb3, Bmp4 and Smurf2) and apoptosis signaling pathways (Casp6, 1500003O03Rik, Prkar1a, Ripk1, Traf2, Capn5, Endog and Myd88). Conclusion Menin may affect mouse embryonic development by several cellular signaling pathways, including Wnt, MAPK, TGF-β and apoptosis signaling pathways.