Many of the developmental anomalies observed in cloned animals are related to fetal and placental overgrowth, a phenomenon known as the “large offspring syndrome” (LOS) in ruminants. It has been hypothesized that the epigenetic control of imprinted genes, i.e. genes that are expressed in a parental-specific manner, is at the root of LOS. Our recent research has focused on understanding the epigenetic alterations to imprinted genes that are associated with assisted reproductive technologies (ART), such as early embryo in vitro culture (IVC) and somatic cell nuclear transfer (SCNT) in cattle. We have searched and identified single nucleotide polymorphisms in Bos indicus DNA useful for analysis of parental-specific alleles and their respective transcripts in tissues from hybrid embryos derived by crossing Bos indicus and Bos taurus cattle. Due to the frequency of placental anomalies in SCNT and in some IVC gestations, our initial studies focused on genes known to be necessary for trophoblast proliferation (Mammalian Achaete Scute-like Homologue 2; ASCL2) and differentiation (Heart and neural crest cell derivative 1; HAND1). ASCL2 was bi-allelically expressed prior to implantation but paternally silenced after implantation. At day 17, SCNT embryos showed more abundant ASCL2 and less abundant HAND1 transcripts. After implantation, SCNT fetal cotyledons displayed higher ASCL2 and HAND1 than AI and IVC tissues. To further investigate epigenetic anomalies, we analyzed the differentially methylated regions of other imprinted genes in cattle, i.e. SNRPN, H19 and the IGF2R. Compared with the patterns observed in vivo (AI), we observed a generalized hypomethylation of the imprinted allele and the bi-allelic expression of embryos produced by SCNT. Together, these results indicate that imprinting marks are erased during the reprogramming of the somatic cell nucleus during early development, indicating that such epigenetic anomalies may play a key role in the mortality and morbidity of cloned animals