Infections caused by free-living amoebae are not so frequent, but often fatal, in immunocompetent as well as in immunocompromised patients. Free-living amoebae could be classified into several different species: Naegleria, Acanthamoeba, Balamuthia and Sappinia. Four different clinical entities are caused by these organisms: PAM (primary amoebic meningoencephalitis), GAE (granulomatous amoebic encephalitis), AK (amoebic keratitis) and disseminated granulomatous amoebic disease. PAM is caused by a free-living amoeba N. fowleri. It usually affects immunocompetent young children and adults, usually after the contact with fresh water. GAE is caused by free-living amoebae from the genus Acanthamoeba and the species Balamuthia mandrillaris and Sappinia pedata. It usually occurs in immunocompromised individuals. AK is caused by free-living amoeba from the genus Acanthamoeba. It occurs in immunocompetent subjects. The predisposing factors for the AK development are corneal trauma and the wearing of contact lenses combined with the insufficient eye-hygiene. Disseminated granulomatous amoebic disease is caused by a free-living amoebae from the genus Acanthamoeba and the species Balamuthia mandrillaris. It usually affects immunocompetent individuals. The diagnosis of infections caused by free-living amoebae is often delayed. The main reason for late diagnosis is insufficient clinical awareness. The current therapeutic algorithms are not satisfactory.