Aberrant gene expression in somatic cell nuclear-transferred (NT) embryos due to abnormal epigenetic modifications of the donor nucleus likely accounts for much of the observed diminished viability and developmental abnormalities. We compared the expression of 13 developmentally important genes in individual 8-cell and blastocyst stage NT embryos produced from adults female cumulus cells and adult male skin fibroblast cells with low and high incidences of neonatal abnormalities. In vitro-fertilized (IVF) embryos were used as control embryos. Among the genes tested, the relative abundance of Glut-1, IGF-1R, E-cad, and Cx43 transcripts varied significantly between the two types of NT embryos at the 8-cell stage. The relative abundance of manganese super oxide dismutase (MnSOD) and Stat3 transcripts was significantly higher in IVF embryos compared with both types of NT embryos. At the blastocyst stage, there was a significant difference in the relative expression of only one gene, Bcl-2, between the two types of NT embryos. Although the level of Glut-1 expression did not vary between the two types of NT blastocysts, its expression in both types of NT blastocysts was significantly lower than that in IVF blastocysts. The MnSOD expression level tended to be higher in NT blastocysts. The gene expression profile for any single gene, however, was highly variable among individual embryos and was independent of embryo morphology. The present study demonstrated that the expression profiles of the 13 genes examined in Day 9 NT blastocysts produced from two different types of donor cells with different incidences of neonatal abnormalities are largely indistinguishable.