A five-month-old Japanese Black calf fed at a farm in Kagoshima Prefecture died as a result of severe diarrhea and dehydration. During necropsy, hyperemia and hemorrhages were found on the mucosa of the jejunum, ileum and rectum. Some Trichuris discolor worms were also obser ved in the mucosa of the rectum. Histopathological examination of the rectum with hemor rhagic enteritis revealed coccidian parasites of various developmental stages in the epithelial cells. Using DNA purified from sections of the rectum, species-specific PCR was conducted and consequently Eimeria (E.) bovis and E. zuernii specific genes were amplified. Through fecal examination of other calves on the farm, oocysts morphologically similar to those of E. bovis and E. zuernii, and eggs of T. discolor were detected. Consequently, we successfully identified E. bovis and E. zuernii from formalin-fixed paraf fin embedded sections and identified a lethal case with these Eimeria species.