Even though all the cells in our organism have the same genome, they are still very different. The cells differ in their sizes, shapes and most important functions. The formation of different cells within the same organism is called cell differentiation. Our control over cell differentiation promises to allow us to perform tremendous medical tricks such as the growth of replacement organs from single cells. However, to control cell differentiation we have to better understand the molecular mechanisms that make the cells with the same genome look and function differently. Comprehensive studies of cell differentiation must be undertaken at the single cell level. The recent progress in single cell studies will be discussed.