Enterovirus A71 (EV-A71) causes severe disease upon systemic infection, sometimes leading to life-threatening neurological dysfunction. In most cases, infection is limited to the gastrointestinal tract, where virus is amplified for transmission. We used three-dimensional epithelial organoids generated from crypt stem cells of healthy patient colon tissue (colonoids) to investigate viral spread. Surprisingly, many infected cells were extruded from the apical surface of colonoids, leading to their removal from the epithelium. EV-A71 infected extruding cells were not frequently apoptotic and could propagate infection to uninfected monolayers and colonoids. Cell extrusion in healthy gastrointestinal epithelium is mediated either by apoptosis or cell-crowding forces sensed via the mechanosensitive ion channel Piezo-1. Treatment of infected colonoids with mechanosensitive ion-channel inhibitor GsMTx4 significantly reduced the infected cell extrusion. Instead, increased abundance of cell-free virus in media was observed. These results suggest a novel mechanism for extrusion of live, virus-infected cells through mechanical compression forces. In the gastrointestinal tract, apically extruded cells are released into the gut lumen and excreted in feces; therefore, extruded infected cells likely contribute to virus spread.