Objectives Despite comprehensive diagnostics, the aetiology of meningoencephalitis (ME) in cats often remains undetermined. As a result of recently published surveys, Encephalitozoon cuniculi has gained growing importance in cats not only with ocular disorders, but also with central nervous system disease. Therefore, it was hypothesised that E cuniculi may be an underestimated pathogen in the development of feline non-suppurative and/or granulomatous ME. Methods As a first step, histopathological sections of the brain of cats with encephalopathy were retrospectively reviewed to identify cases of granulomatous ME. In a second step, an immunohistochemical screening for detection of E cuniculi was performed in cases with ME of unknown origin. Results In 59/89 (66.3%) cats with ME, an aetiologically relevant pathogen was detected. Forty-three of 89 (48.3%) cats had a diagnosis of feline infectious peritonitis. In 14/89 (15.7%) cats, protozoan cysts were identified and infection with Toxoplasma gondii was confirmed by immunohistochemistry (IHC) in all cases. In 2/89 (2.3%) cats with granulomatous ME, fungal organisms were identified. Thirty of 89 (33.7%) cats with ME of unknown origin that underwent IHC for the detection of E cuniculi remained negative. Conclusions and relevance The results of this study suggest that E cuniculi is unlikely to be directly associated with (non-suppurative and/or granulomatous) ME in cats in Austria.