Induced pluripotent stem cells (iPSCs) are generated by reprogramming mouse or human somatic cells to a pluripotent state by introducing key transcription factors and have great therapeutic potential. It has been illustrated that the transcriptional and post-transcriptional profiles of nuclear-transferred embryonic stem cells (ntESCs) is identical to those of embryonic stem cells derived from fertilized blastocysts (fESCs). Although iPSCs seem to be indistinguishable from fESCs, the degree of transcriptomic and proteomic similarity among iPSCs, ntESCs, and fESCs has not yet been elucidated completely. To investigate whether iPSCs and fESCs have similar therapeutic potential, we compared mRNA and protein pro?les of mouse iPSC, ntESCs, and matching fESCs lines using microarray technology, iTRAQ method, and bioinformatic analyses. Real-time PCR, two-dimensional LC, and MS/MS analyses were further conducted to study the expression of speci?c transcripts and identify and quantitate 929 proteins. Our results demonstrate that, like ntESCs, the iPSC and matching fESCs lines have very similar transcriptional and protein expression profiles. This is consistent with their similar developmental potential.