Induced pluripotent stem cells (iPSCs) are somatic cells that have been reprogrammed to a pluripotent state via introduction of defined transcription factors. iPSCs are a valuable resource for regenerative medicine, but whether iPSCs are identical to embryonic stem cells (ESCs) remains unclear. In this study, we performed comparative proteomic analyses of human somatic cells [human newborn foreskin fibroblasts (hFFs)], human iPSCs (hiPSCs) derived from hFFs, and H9 human ESCs (hESCs). We reprogrammed hFFs to a pluripotent state using 4 core transcription factors: Oct4 (O), Sox2 (S), Klf4 (K), and c-Myc (M). The proteome of hiPSCs induced by 4 core transcription factors was relatively similar to that of hESCs. However, several proteins, including dUTPase, GAPDH, and FUSE binding protein 3, were differentially expressed between hESCs and hiPSCs, implying that hiPSCs are not identical to hESCs at the proteomic level. The proteomes of iPSCs induced by introducing 3, 5, or 6 transcription factors were also analyzed. Our proteomic profiles provide valuable insight into the factors that contribute to the similarities and differences between hESCs and hiPSCs and the mechanisms of reprogramming.