A total of 48 intestinal samples of new born alpacas which died due to diarrhea proceses were evaluated. Samples collected during the dry season (June-August, 2002) were from animals belonging to the Experimental Research Station of IVITA, La Raya, Cusco, and those collected during the parturition season (February, 2003) were from a farmers community tn Nuñoa, Puno. Topographic intestinal samples were taken, fixed in 15% formalinen solution and stained with H-E. Thirty seven cases were compatible with bacterial processes, where 30 of them were due to enterotoxemia and the other 7 were processes complicated with colibacilosis. Only two of these cases were associated with Cryptosporidium sp. Four cases were related with Eimeria macusaniensis and enterotoxemia and 7 cases with E. macusanensis and E. punoensis. Only 4 cases were observed in association with E. lamae. This is the first report of intracellular forms of E. ivitaensis in Lieberkhün glands of yeyuno and ileum, and extracellular forms of E. macusaniensis in smal intestine, cecal and ascendent colon.