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We report two cases of unclear granulomatous encephalitis where pathogenic algae, genus Prototheca, were identified as causative agent. Granulomatous encephalitis is - after exclusion of cause - per definition diagnosed and managed as neurosarcoidosis. However, protothecal infections go undetected by standard bacterial and fungal rDNA screening. As cerebral protothecosis is potentially treatable, raising awareness for this condition is relevant, because therapeutic immunosuppression is to be avoided. This article is protected by copyright. All rights reserved.