Gene expression profiling of compromised umbilical cords (CUCs) derived from somatic cell nuclear transfer (scNT) clones was performed to determine why scNT-derived clones often exhibit malformed umbilical arteries. Umbilical cord samples were obtained from 65 scNT piglets, and of these, nine displayed a CUC. Microscopic analyses of the scNT clones with CUCs (scNT-CUCs) revealed complete occlusive thrombi that were not detected in the arteries of scNT clones with normal umbilical cords (scNT-Ns). Moreover, whereas the allantoic ducts of the scNT-Ns contained columnar epithelium, the scNT-CUCs lacked this epithelial layer. Compared to scNT-Ns, the scNT-CUCs exhibited severe histological damage, including tissue swelling and vein and arterial damage with complete occlusive thrombi. To investigate functional abnormality, gene expression profiles were created in duplicate using the Platinum Pig 13K oligonucleotide microarray, which contains 13,610 probes of 70 bp in length and is capable of interrogating 13,297 targets with up to one probe per target. Probe sets were selected according to a 2-fold or greater increase or decrease of gene expression in scNT-CUCs compared to scNT-Ns. Most genes expressed in scNT-Ns were also expressed by scNT-CUCs. However, most genes involved in transcriptional regulation, such as JUN, JUNB, and FOSL2, showed a significant decrease in expression in the scNT-CUCs, which may produce a ripple effect capable of altering the transcriptomes of many other cellular processes, including angiogenesis, antioxidation, and apoptosis. The scNT-CUCs with thrombosis showed extensive apoptosis leading to placental insufficiency and related pathology. Considering that the umbilical cord plays a role in the transportation of metabolites to the fetus, placental insufficiency in scNT-CUCs may be caused by an increase in apoptotic protein expression from scNT-derived umbilical cords with hypoplastic arteries, and our results provide evidence that porcine oligonucleotide microarray analysis is a useful tool for screening scNT-derived abnormalities in pigs.