Recent studies have been raising doubts on the safety of induced pluripotent stem cells (iPSCs) and proposing that the process of reprogramming brought about copy number variations (CNVs) in iPSCs. However, a recent paper published in Nature provided evidence showing that most CNVs were pre-existed as somatic mosaicism but not resulted from the reprogramming. This new finding would profoundly reshape some previous thoughts and endorse the confidence of iPSCs in both research and therapy.