Gills from Atlantic salmon with experimentally induced amoebic gill disease (Neoparamoeba spp.) were examined with transmission electron microscopy to assess pathology and host-cell responses. Amoebae were found either on the surface epithelium or with pseudopodia extending deeply into invaginations of epithelial cells. The amoebae had various densities along the plasma membrane and contained electron-dense deposits within their cytoplasm. Surface epithelial cells sloughed from the gills and had features consistent with apoptosis, including rounded shape, loss of surface microridges, and hypercondensation of nuclear chromatin. Affected areas of gills had fusion of secondary lamellae with interlamellar spaces occupied by mitotic epithelial cells and eosinophils. Eosinophils contained abundant fusiform-shaped granules that measured approximately 1 μm long and 360 nm wide. The granule consisted of an electron-dense matrix with a central inclusion that was less electron-dense, consisting of particulate and fibrillar material. In many instances, the central inclusion appeared empty and 90% of the eosinophils had morphology suggestive of piecemeal degranulation. Also observed within affected areas were a few neutrophils, mucous cells releasing mucus, and a small number of dendritic-like cells.