Long-lived and self-renewing adult stem cells (SCs) are essential for homeostasis in a wide range of tissues and can include both rapidly cycling and quiescent (q)SC populations. Rapidly cycling SCs function principally during normal tissue maintenance and are highly sensitive to stress, whereas qSCs exit from their quiescent state in response to homeostatic imbalance and regenerative pressure. The regulatory mechanisms underlying the quiescent state include factors essential for cell cycle control, stress response and survival pathways, developmental signalling pathways, and post-transcriptional modulation. Here, we review these regulatory mechanisms citing observations from the intestine and other self-renewing tissues. © 2015 The Authors. The Journal of Physiology © 2015 The Physiological Society.