Stem cells possess a great potential of differentiating into various types of cells. They are capable of sustaining their stemness or getting converted into cells having a more specialized function in the body. The obstacles that pose as a barrier to the therapeutic and clinical applications of stem cells are the difficulty in deriving and controlling the fate of these stem cells. With the advancement of science and technology and with better knowledge, scientists have come up with the method of reprogramming for the generation of iPSCs. Reprogramming refers to converting a differentiated cell into its embryonic state, capable of re-differentiating into other cell types. These iPSCs phenotypically as well as morphologically resemble ESCs. Induced pluripotent stem cells are of great advantage for studying the pathogenesis of disease and drug discovery. Understanding the regulation of stem cells is of great importance so as to generate a controlled stem cell fate and function. A safe, more efficient and a cost-effective approach to this is the use of small molecules for reprogramming. Small molecules are easier to handle and provide a good tool for use in in vitro and in vivo studies for the development of therapeutics. Recently, fine-tuning of various combinations and concentrations of the small molecules helps provide control over the regulation of iPSCs and the reprogramming outcomes. In this article, we review patents and discuss the recent development with respect to the use of small molecules, their control over the cell fate, the effect on regulation of the reprogramming factors and the efficiency of reprogramming.