Passerines are frequently parasitized by coccidia, especially species of the genus Isospora, with extra-intestinal stages that can be highly pathogenic causing serious clinical damage in young birds. Whilst there is still no effective treatment to completely clear isosporoid coccidia with extra-intestinal stages from a host species, our results showed that prolonged treatment with toltrazuril (BAYER AG, Leverkusen, Germany) can decrease the oocysts in faeces and thus reduce the extra-intestinal phase of the infection. The toltrazuril treatment is therefore probably indirectly effective against the systemic form of atoxoplasmosis.