Tissue engineering approaches for expanding, differentiating and engrafting embryonic or adult stem cells have significant potential for tissue repair but harnessing endogenous stem cell populations offers numerous advantages over these approaches. There has been rapid basic biological progress in the identification of stem cell niches throughout the body and the molecular factors that regulate their function. These niches represent novel therapeutic targets and efforts to use them involve the familiar challenges of delivering molecular medicines in vivo. Here we review recent progress in the use of genes, proteins and small molecules for in situ stem cell control and manipulation, with a focus on using stem cells of the central nervous system for neuroregeneration.