Induced pluripotent stem (iPS) cells, obtained from reprogramming somatic cells by ectopic expression of a defined set of transcription factors or chemicals, are expected to be used as differentiated cells for drug screening or evaluations of drug toxicity and cell replacement therapies. As pluripotent stem cells, iPS cells are similar to embryonic stem (ES) cells in morphology and marker expression. Several types of iPS cells have been generated using combinations of reprogramming molecules and/or small chemical compounds from different types of tissues. A comprehensive approach, such as global gene or microRNA expression analysis and whole genomic DNA methylation profiling, has demonstrated that iPS cells are similar to their embryonic counterparts. Considering the substantial variation among iPS cell lines reported to date, the safety and therapeutic implications of these differences should be thoroughly evaluated before they are used in cell therapies. Here, we review recent research defining the concept of standardization for iPS cells, their ability to differentiate and the identity of the differentiated cells.