The activity and behavior of stem cells is governed by a complex network of molecular pathways. At the heart of these pathways are the genes from DNA that code for the large molecules that act in this network. One way to regulate these networks is simply for the cell to control the quantity of product produced by individual genes. Recent work, however, has also shown that the same gene can code for different products depending on how that gene is read. In this review, we focus on a type of molecular regulation called alternative polyadenylation, which controls the length of the product, and discuss the impact of this process on stem cell biology as well as areas for future research.