The efficiency of nuclear transfer was evaluated in vitro and in vivo using non-transgenic and transgenic cloned bovine embryos. In addition, in order to better understand the low pre- and post-implantation development observed in transgenic nuclear transfer embryos, a gene expression data analysis was conducted in this group. We observed no difference (P > 0.05) in the cleavage rate of nuclear transfer embryos generated with transgenic and non-transgenic fetal fibroblasts. However, the blastocyst rate was affected (P < 0.01) in transgenic (13%) compared to non-transgenic nuclear transfer embryos (24%). Despite this difference, the quality of embryos as assessed by the total number of cells and morphological appearance was not different (P > 0.05). Pregnancy rate was also affected (P < 0.05) in transgenic (7%) compared to non-transgenic nuclear transfer embryos (43%), though all pregnancies failed to maintain to term. Gene expression data analysis revealed a decrease (P < 0.05) of INF-τ and HDAC1 in transgenic nuclear transfer embryos relative to embryos generated by in vitro fertilization. Considering the importance of these two genes in maternal recognition of pregnancy and nuclear reprogramming, the alterations observed in these transgenic embryos might help to explain the low pre- and post-implantation development observed in this group, which highlights the need to assess different donor cells before embryo transfer, particularly when the aim is to generate transgenic offspring.