The aim of the study was to investigate the presence, distribution and density of major histocompatibility complex (MHC) class II+ cells in the ocular tissues of the Atlantic salmon, Salmo salar, prior to and following vaccination. Eyes were collected 14 days prior to and at 4, 11, 25 and 39 days and 4 months subsequent to vaccination with a commercial fish vaccine. A quantitative analysis was performed in sections on the number of immunopositive cells in the retinal layers. In all groups, MHC class II+ cells were detected in the area of the limbus but not in the central parts of the cornea. In the uvea, immunopositive cells were present in unvaccinated and vaccinated fish. Abundant immunopositive cells were identified in the choroid rete (or choroid gland) in all groups as well as in the ventral ciliary cleft, where macrophage-like MHC class II+ cells were seen. Quantitative histology of the retina revealed a significant increase in MHC class II+ cells in the outer plexiform layer (OPL) and the inner nuclear layer (INL) 4 days following vaccination. Positive cells were detected in all layers of the retina with the exception of the photoreceptor layer.