Nine of 23 (39%) research ewes with severe diarrhea and weight loss had histologic lesions consistent with Eimeria gilruthi infection in their abomasa. Gross anatomic lesions included hundreds of opaque 1-mm nodules in abomasal mucosa that corresponded microscopically to 200–300 µm diameter organisms surrounded by areas of necrosis. Analysis of fecal samples from 4 ewes demonstrated oocysts from typical ovine Eimeria species, none of which were E. gilruthi. Two separate PCR reactions were performed on abomasal tissue from 4 sheep to amplify the 18S ribosomal DNA (rDNA) and internal transcribed spacer (ITS) region of the rDNA, respectively. The resultant 18S rDNA nucleotide sequences shared 99% homology with multiple Eimeria species in GenBank. The ITS region shared 77% homology with E. ellipsoidalis in GenBank. Further studies are needed to understand the life cycle and pathogenicity of E. gilruthi. Our results underscore the inclusion of E. gilruthi in the differential diagnosis of diarrhea and weight loss in sheep.