Toxigenic types of Clostridium perfringens are significant causative agents of enteric disease in domestic animals, although type E is presumably rare, appearing as an uncommon cause of enterotoxemia of lambs, calves and rabbits. We report herein the typing of 23 C. perfringens strains, by the polymerase chain reaction (PCR) technique, isolated from small intestine samples of bovines that have died suddenly, after manifesting or not enteric or neurological disorders. Two strains (8.7%) were identified as type E, two (8.7%) as type D and the remainder as type A (82.6%). Commercial toxoids available in Brazil have no label claims for efficacy against type E-associated enteritis; however, the present study shows the occurrence of this infection. Furthermore, there are no recent reports on Clostridium perfringens typing in the country.