The microsporidia Encephalitozoon intestinalis is an opportunistic pathogen responsible for severe gastrointestinal diseases and disseminated infection in AIDS patients. No light-microscopical method allows the specific detection of this unicellular parasite and up to this date, only electron microscopy could confirm the diagnosis of the species. We propose a method combining the non specific labelling of microsporidian spores by the fluorochrome Uvitex 2B and an indirect immunofluorescent assay with a polyclonal antibody specifically directed against E. intestinalis. Preliminary data demonstrate the specificity of this antibody. This method enables the distinction between E. intestinalis and Enterocytozoon bieneusi an other microsporidian also associated with gastrointestinal infection. Due to the precocious detection of E. intestinalis patients will be treated earlier with albendazole which is potentially active against this species.