The free-living amoebae are a group of organisms that are distributed around the world and commonly inhabit different aqueous media. Medical importance for the human being are among others, Acanthamoeba spp. and Naegleria fowleri. Acanthamoeba castellanii may cause infection in the skin and lung, as well as occasionally granulomatous encephalitis and is the etiologic agent responsible for eye infection, amoebic keratitis of the cornea that not treated on time and properly puts at risk the patient view. Naegleria fowleri is the causal agent of almost always fatal acute infection, primary amoebic meningoencephalitis that occasionally infects the human and other mammals. Currently, we studied some aspects of these amoeba cell biology, such as the comparative study of the mechanisms of pathogenicity on monolayers of MDCK cells, corneas of hamster and ultrastructural characterization of their surface by means of specific markers. In addition, studies are done to carry out the morphological identification and extent of in vitro pathogenicity of amoebae isolated from clinical cases related to amoebic keratitis.