A case of intranuclear coccidiosis in an 11-month-old female Japanese Black calf is described. Because the calf exhibited diarrhea and failure to grow and then became moribund, euthanasia was performed. Histologically, the small intestinal villi were highly atrophic, and the epithelial cells frequently had meronts or merozoites within the nuclei. A few intranuclear gametocytes were also seen. The presence of Eimeria alabamensis-specific DNA in the lesions was demonstrated by polymerase chain reaction and nucleotide sequence analyses. Electron microscopy disclosed that most parasites were within nuclear inclusions encircled by the two membranes derived from the nuclear envelope, and that intracytoplasmic meronts and merozoites were in direct contact with the cytosol. Apparently, mature merozoites could be free without destruction of the host cells, and this may be associated with the relatively low pathogenicity of this coccidium.