Abnormal development and fetal loss during the post-implantation period are key concerns in the production of cloned animals by somatic cell nuclear transfer (SCNT). We hypothesized that the problems in cloned porcine offspring derived from SCNT are related to interactions between the conceptus and the endometrial environment. In the present study, we investigated expression patterns in the formation of placenta-related genes (Cdx2 and GATA6) in whole in vivo normal porcine embryos (from single cell to blastocyst) and each tissue of a normal fetus at Days 25, 35 and 55 by quantitative mRNA expression analysis using real-time PCR. The expression of Cdx2 and GATA6 mRNA increased to around the blastocyst stage. These genes were gradually decreased from the peri-implantation to post-implantation stage. Moreover, we examined the expression patterns of Cdx2 and GATA6 in Day 35 normal and SCNT cloned fetuses by the same methods. And, the level of Cdx2 and GATA6 gene expression in the extraembryonic tissue of SCNT was significantly higher than that of control tissues. From the present results, it can be postulated that the aberrant expression of Cdx2 and GATA6 genes in the endometrial and extraembryonic tissues at pre- and peri-implantation stages may be closely related to the lower efficiency of animal cloning.