The intestinal epithelium is renewed every 3–5 days from at least two principal stem cell pools. Actively cycling crypt based columnar (CBC) Lgr5+ cells and slower cycling Bmi1-expressing or Krt19-expressing cells maintain the small intestinal and colonic epithelium in homeostasis and injury. Following acute epithelial damage, Lgr5+ stem cells are susceptible to injury and a reserve stem cell or progenitor pool is responsible for regeneration of the epithelium. Current data suggests that intestinal stem cells respond to inflammatory signals to modulate their expansion during epithelial regeneration. Here, we review how inflammation and injury affect intestinal and colonic stem cells.