Differentially regulated proteins within porcine somatic cell nuclear transfer (SCNT)-derived conceptuses were compared with conceptuses that were derived from natural matings on day 14 of pregnancy. Proteins that were expressed prominently on day 14 were identified in SCNT-derived conceptuses using 2-D PAGE and MALDI-TOF MS. Sixty eight proteins were identified as being differentially regulated in the SCNT-derived conceptuses. Among these, 62 were down-regulated whereas the other six proteins were up-regulated. Glycolytic proteins, such as pyruvate dehydrogenase, malate dehydrogenase and lactate dehydrogenase, were down-regulated in the SCNT-derived conceptuses whereas apoptosis-related genes as annexin V, Hsp60, and lamin A were up-regulated. Thus, apoptosis-related genes are expressed at significantly higher levels in the SCNT-derived conceptuses than in the control conceptuses, whereas metabolism-related genes are significantly reduced.