A novel coccidian parasite from the kidney of big brown bats (Eptesicus fuscus) is described. This coccidian (Nephroisospora eptesici nov. gen., n. sp.) was associated with a generally mild, focal or multifocal, well-demarcated cortical renal lesion less than 1 mm in diameter. The lesion represented cystic, dilated tubules with hypertrophied tubular epithelial cells and was present in the kidneys of 29 of 590 bats. Numerous coccidian parasites in various stages of development were present within the tubular epithelial cells and within the cyst lumina. Oocysts were collected from cystic dilated tubules. Thin-walled, sporulated ellipsoidal oocysts measuring an average of 18.9 × 20.8 µm were present in kidney tissue. The oocysts contained 2 sporocysts with 4 sporozoites. A polar body and a prominent oocyst residuum were present in the oocysts, but no micropyle, sporocyst residuum, or Stieda bodies were detected. Analysis of the 18S rRNA gene sequence put the parasite in the Sarcocystidae. The parasite is closely related to Besnoitia, Hammondia, Neospora, and Toxoplasma. Ultrastructural features, such as the presence of an apical complex in merozoites, support the identification of a coccidian. A new genus and species, Nephroisospora eptesicii, is proposed for this unusual coccidian in which the entire cycle is completed in the kidney of a single host; it has a membrane-like oocyst wall, sporogony occurs in the host rather than in the abiotic environment, and the positioning of the parasite by nucleic acid sequence indicates it to be closely allied to Sarcocystis and Besnoitia.