Eimeria arundeli is a widespread coccidian parasite of the common wombat (Vombatus ursinus), and has been considered to be nonpathogenic. We describe disease in two captive juvenile wombats ascribed to infection with E. arundeli. One animal had diarrhea, the second had mucoid soft feces and lost weight over several weeks prior to death. Masses of coccidial gametocytes in hypertrophic cells in the lamina propria distended villi, causing grossly visible raised pale thickened regions over extensive areas of the mucosa of the small intestine in both animals. Neutrophils infiltrated affected mucosa, and there was an inflammatory exudate into the intestinal lumen in case one. In case two, neutrophils infiltrated the lamina propria of villi focally, crypts were distended by necrotic debris, and epithelium on villi was extremely attenuated. No bacterial pathogens were isolated from lung and intestine in case one; case two was not cultured. Oocysts consistent with E. arundeli were present in large numbers in floatations of diarrheic feces in both cases.