The seminal report from Takahashi and Yamanka in 2006 describing the reprogramming of somatic cells to induced pluripotent stem (iPS) cells [1] marked the beginning of a new field of research, resulting in hundreds of publications in a short 3 years. Among other things, the promise of iPS cells in cell therapy circumvents many of the ethical concerns associated with embryonic stem (ES) cell research, and autologous patient-specific cells can be generated. Nonetheless, the jury is still out on the extent to which iPS cells and ES cells are functionally equivalent. This review focuses on the genetic and functional comparisons between these two cells types.