Mouse parthenogenetic (PG) embryos do not survive beyond day 9.5 of pregnancy. In this study, to understand the molecular mechanisms underlying the failure of parthenogenesis at the early developmental stage, we performed global gene expression profiling of the PG inner cell mass (ICM) and trophectoderm (TE) using microarray analysis, compared the results with those from in vitro-fertilized embryos, and identified genes whose expression levels showed more than a 4-fold change as a cutoff. Eighty probe sets were up-regulated and 59 probe sets down-regulated in the PG ICM, while 169 and 43 probe sets were respectively up-regulated and downregulated in PG TE. We selected two genes (Sfmbt2 and Gab1) that were down-regulated in both the PG ICM and TE, one gene (Nat1) that was down-regulated in the PG ICM, and one gene (Lysmd2) that was up-regulated in the PG TE, and analyzed the gene expression levels using real-time PCR. The quantitative expression levels of these four genes were confirmed by real-time PCR. In the present study, we identified differentially expressed genes in PG embryos and also identified those that were ICM- or TE-specific in PG embryos.