The mechanisms of nuclear reprogramming following somatic cell nuclear transfer (SCNT) to enucleated oocytes or factor-based reprogramming are poorly understood. In this study global transcriptional analysis was performed on a number of different rhesus monkey (Macaca mulatta) cell and tissue samples, including rhesus-induced pluripotent stem cells (IPSCs) and rhesus SCNT-derived embryonic stem cells (SCNT-ESCs). Global transcriptional cluster analysis and stem cell-specific gene expression analysis both suggested that the oocyte-reprogrammed SCNT-ESCs were transcriptionally closer to the control fertilized ESCs than IPSCs. These results, combined with previous epigenetic analysis studies in the mouse, reinforce the hypothesis that oocyte-reprogrammed cell nuclei are more completely reprogrammed to an ESC state than IPSCs. Transcriptional analysis of rhesus oocytes detected over 500 ESC-specific genes, including OCT3/4, NR5A2, and DNMT3B. These results, combined with previously published reprogramming research, were used as the basis for a general model to explain the mechanisms of nuclear reprogramming.