Simple SummaryEncephalitozoonosis is a common infectious disease widely spread among rabbits. Its causative agent, Encephalitozoon cuniculi, is considered to be transmissible to humans. In rabbits, clinical signs include discoordination, head tilt, excessive water intake, excessive urination and cataracts. This study investigates, for the first time, whether the E. cuniculi organism can be detected in ocular structures in healthy adult rabbits after experimental oral infection using immunohistochemistry—detection of the organism in the tissue using a specific staining method. In infected animals, E. cuniculi spores were detected in many ophthalmic structures (periocular connective tissue, sclera, cornea, choroidea, iris, retina and lens) as early as 2 weeks after infection. There were no signs of inflammatory lesions in any of the ocular tissues examined at 2, 4, 6 and 8 weeks after infection. E. cuniculi was also detected in the lens of adult rabbits, which indicates that ways of lens infection other than intrauterine and haematogenic are possible. This information can help to understand E. cuniculi dissemination to various ocular tissues structures after oral infection.Encephalitozoonosis is a common infectious disease widely spread among rabbits. Its causative agent, Encephalitozoon cuniculi, is considered as a zoonotic and emerging pathogen capable of infecting both immunocompetent and immunocompromised hosts, including humans. In rabbits, clinical signs include neurological, kidney and ocular disease. The aim of this study was to detect E. cuniculi in ocular structures in immunocompetent rabbits after experimental oral infection using immunohistochemistry. In infected animals, E. cuniculi spores were present in periocular connective tissue, sclera, cornea, choroidea, iris, retina and lens, as a round to ovoid organism reacting with a specific anti-E. cuniculi monoclonal antibody as early as 2 weeks after infection. There were no signs of inflammatory lesions in any of the ocular tissues examined at 2, 4, 6 and 8 weeks after infection. In the present study, E. cuniculi was also detected in the lenses of adult rabbits, which indicates that ways of lens infection other than intrauterine and haematogenic are possible.