Free-living amoebae (FLA) belonging to Acanthamoeba and Sappinia genera as well as Balamuthia mandrillaris and Naegleria fowleri species are aerobic, mitochondriate, eukaryotic protists that occur worldwide and can potentially cause infections in humans and other animals (Visvesvara and Maguire, 2006; Visvesvara et al., 2007). Due to the fact that these amoebae have the ability to exist as free-living organisms in nature and only occasionally invade a host and live as parasites within host tissue, they have also been called amphizoic amoebae (Page, 1988). All four amoebae are known so far to cause infections of the central nervous system (CNS). Several species of Acanthamoeba (i.e. A. castellanii, A. culbertsoni, A. hatchetti, A. polyphaga, A. rhysodes), the only known species of Balamuthia, B. mandrillaris, two species of Sappinia genus, S. diploidea and S.pedata, and only one species of Naegleria, N. fowleri, are known to cause disease in humans and other animals (Khan, 2006; Visvesvara et al., 2007).