Cloning by somatic cell nuclear transfer (SCNT) in pigs has great value for research and biomedical applications. However, cloning pigs is inefficient, and cloning procedures often lead to the birth of abnormal offspring because of the inadequate nuclear remodeling of donor cells as well as inadequate subsequent development. To understand the problems of the cloning process, it is necessary to understand how the uterus interacts with cloned embryo during pregnancy and supports placentation and fetal development. In this study, we compared gene expression profiles of the uterus with SCNT embryos to those of the uterus with normal embryos by natural mating. We obtained the uterine endometrial tissues on day 30 of pregnancy and conducted gene expression profiling using the Platinum Pig 13K oligonucleotide microarrays. Of the 13,610 genes analyzed, expression of 351 genes significantly increased or decreased in the uterine tissues with SCNT embryos compared to those with normal embryos. The differentially regulated genes included enzymes involved in steroidogenesis and extracellular matrix remodeling and uterine secretory proteins. Analyses of real-time reverse transcription-polymerase chain reaction (RT-PCR) and in situ hybridization of selected genes confirmed the validity of the gene expression patterns observed in the microarray analysis. Results of this study showed that the transcriptional profile of the genes in the uterus with SCNT embryos was regulated differently indicating that the maternal responsiveness to the SCNT embryos was impaired, resulting in the altered gene expression in the uterus and, in turn, abnormal placental and fetal development and increased embryonic loss.