Histopathological analysis of 108 intestine samples (103 grossly affected ileum and 5 jejunum) taken from Clostridium-induced neonatal alpaca (Vicugna pacos) enterotoxemia mortalities collected in the Departments of Arequipa, Puno and Cusco of southern Peru during the 2005-2008 birth seasons (January-March), revealed the presence of large numbers of both asexual and sexual stages of Eimeria macusaniensis in 33/108 (30.55%) of the samples with moderate to severe necrotized and/or hemorrhagic enteritis. It is proposed that damage to the mucosa produced by coccidial infections may facilitate overgrowth of Clostridium perfringens with toxin production leading to fatal enterotoxemia.