The initial stages of Naegleria fowleri meningoencephalitis in mice were immunohistochemically characterized following the first 8 h post-intranasal inoculation. The events found after 8 h were: (1) amebas in contact with the mucous layer of the olfactory epithelium, (2) numerous parasites eliminated by extensive shedding of the mucous layer, and (3) many organisms reaching the nasal epithelium. In contrast to other works, we observed that after 24 h, amebas invaded the epithelium, without evidence of the disruption of the nasal mucosa. In addition some trophozoites invading through the respiratory epithelium were observed, suggesting an additional invasion route. The inflammatory response detected was scarce until 30 h post-inoculation. After 96 h, the inflammatory response was severe in the olfactory bulb and brain, and the tissue damage great. Consequently, an inflammatory reaction may enhance tissue damage but apparently does not destroy amebas which seem to proliferate in the olfactory bulb.