The generation of induced pluripotent stem (iPS) cells from somatic cells can be a useful tool for regenerative medicine. The artificial nature of iPS cells raises concerns whether iPS and embryonic stem (ES) cells, are molecularly and functionally comparable. In this study we generated iPS cells using a genomic integration free method, and using the advance of proteomics, we aimed to elucidate any differences in the protein profile between iPS and ES cells, in terms of pluripotency and differentiation potential to vascular cell lineages. The results demonstrated that 180 proteins were differentially expressed, in which 66% showed a decreased expression pattern in iPS cells. Functional classification analysis revealed that these proteins were associated with mRNA processing, energy metabolism, cytoskeleton, proliferation, and differentiation. Further experiments demonstrated that iPS cells have a decreased proliferation capacity when compared to ES cells. Importantly, iPS cells also displayed a greater potential to differentiate into smooth muscle and endothelial cell lineages, when compared to ES cells. When iPS and ES cells were seeded on collagen IV-coated dishes and cultured with differentiation media, MEM supplemented with 10% serum, iPS cells displayed a differentiation morphology as early as day 3 in comparison to ES cells, and real-time PCR data confirmed that iPS express smooth muscle cell markers such as SMA, calponin, and SM22 in higher levels. When vascular endothelial growth factor (VEGF) was added to differentiation media, iPS cells expressed endothelial markers such as CD31, CD144, Flk-1 and Flt-1 as early as day 3 on differentiation, while ES cells showed limited expression of these markers during the early stages of differentiation. Therefore, identifying differentially regulated protein expression between the two cell types and the pathways they influence, will allow us to elucidate the mechanisms that lead to vascular cell differentiation, thus making iPS technology a successful tool for regenerative medicine and treatment of vascular diseases.