A number of lower vertebrates including urodele amphibians and teleost fish are remarkably adept at repairing and regenerating damaged tissues and organs. Freshwater planarians are even more amazing, capable of regenerating entire body plans from small amputated fragments. In contrast, mammalian regenerative capacity is quite limited but of intense interest, especially related to human health and disease. For those organisms capable of robust regeneration, a common theme is the use of stem cells to replace complex tissues. Key questions remain as to the origin of these cells, whether there are pools of such cells that migrate to injured regions or whether they are generated on site. Beyond their origin, how are the genetic pathways that enable differentiation into multiple cell types and tissues regulated? microRNAs (miRNAs) are small noncoding RNAs that have recently been shown to play important roles in controlling stem cell self-renewal, proliferation and differentiation. Some of these are thought to be required to maintain "stemness". Here, we summarize recent work on the role of miRNAs in stem cells and their roles during regeneration.