Intestinal ischemia and reperfusion injury (IRI) is a deadly and common condition. Death is associated with sepsis due to insufficient epithelial repair, requiring stem cell-driven regeneration, typically beginning 48 hours after injury. Animal models are critical to advancing this field. To effectively study epithelial healing, models must survive clinically relevant intestinal ischemic injury extending to the crypt. Though mouse models are indispensable to intestinal research, their application for studying epithelial repair following severe IRI may be limited. Ischemic injury was induced in mouse and porcine jejunum for up to 3 hours, with up to 72 hours of reperfusion. Histologic damage was scored by Chiu-Park grade and animal survival was assessed. Findings were compared between species. A mouse IRI literature review was performed to evaluate the purported degree of injury, duration of recovery, and reported survival rates. In mice and pigs, 3 hours of ischemia induced severe, reliable injury extending into the crypt. However, at 48 hours, mouse survival was only 23.5% compared to 100% survival in pigs. In literature, ischemia was induced for >1 hour in only 4 of 102 mouse studies and none to 3 hours. Recovery was attempted for 48 hours in only 6 reports. 47 studies reported intestinal crypt injury. Of those that featured histologic intestinal crypt damage, survival rates at 48 hours ranged from 10-50% (median 30%). Mouse models are not ideal to study intestinal stem cell mediated recovery from severe IRI. Alternative large animal models, like pigs, are recommended.