Primary amoebic meningoencephalitis (ME) by Naegleria fowleri a free-living protozoon found in fresh, warm waters, is a well known fatal disease lasting less than one week. It affects sporadically swimmers and children playing in mud puddles. Less than 100 cases have been described. Recently a more rare, distinct amoebic meningoencephalitis due to some species of free-living Acanthamoeba was identified, lasting some weeks or more but still with a fatal evolution. In this case the amoebae do not always enter the brain directly through the cribrous membranes but cause mild, primary infections of respiratory airways: exceptionally, mainly in immunodepressed subjects, they then reach the CNS causing a secondary ME. Naegleria is fairly sensitive in vitro to some drugs, but in vivo their efficacy is dramtically lowered for pharmacokinetic reasons. Acanthamoeba is in every respect less sensitive. Prophylaxis is almost impossible to achieve. Some diagnostic procedures are described and the importance of their use in diagnosis of the so called aseptic purulent ME is stressed.