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Encephalitozoon cuniculi can cause latent disease, especially in lagomorphs and many wild and domestic animals in various countries. This infection is important for veterinary and public health because it is caused by a potentially zoonotic and opportunistic pathogen. The aim of this study was to investigate the relationship between seropositivity of E. cuniculi and renal function markers, which may be useful in predicting the disease in clinically healthy rabbits. In this study, the seropositivity of E. cuniculi infection in clinically healthy rabbits was determined, and necropsy findings were evaluated along with the results of renal function tests. In a laboratory rabbit breeding facility, enzyme-linked immunosorbent assay (ELISA) tests showed that 48 (49.5%) of 97 rabbits were seropositive against E. cuniculi. Blood urea nitrogen (BUN) and creatinine levels were significantly elevated in seropositive animals. Two seropositive rabbits were necropsied to confirm the infection. According to histopathological findings in the kidney, degenerative changes and E. cuniculi spores were identified in the tubule epithelia. Serum creatinine (p |