Leukocyte populations within the kidney, spleen, posterior intestine and gills of Atlantic halibut were investigated using a panel of histological, enzyme- and immunohistochemical methods. In the kidney and spleen, a diverse population of leukocytes was associated with the extensive network of sinusoids and larger blood vessels present in these tissues. IgM+ cells (B-cells, plasma cells and IgM-bearing macrophages) and large mononuclear cells showing reactivity for non-specific esterase (NSE) and acid phosphatase (ACP), representing macrophage populations, were often associated with vessel walls that were also the site of trapping of fluorescent microspheres. In the kidney, trapping of 0.1 and 0.5 μm diameter microspheres occurred at these sites but in the spleen, the 0.1 μm diameter microspheres were retained in ellipsoids. The lymphoid tissues of the kidney and spleen possessed a spread population of 5′-nucleotidase+ (5′N+) cells but compartmentalisation of the splenic white pulp was suggested by an absence of these 5′N+ reticular cells in areas associated with melanomacrophage accumulations and in areas rich in IgM+ cells. A striking feature of the mucosal tissues was the diversity of leukocyte populations within the epithelium particularly of the posterior intestine, including IgM+ cells and NSE+, ACP+ and 5′N+ mononuclear cells. Although limited in numbers in the posterior intestine, IgM+ cells were more common in the epithelium than in the lamina propria. In the gills, leukocytes as detected by enzymatic reactivity were scarce, but IgM+ cells were very abundant in the stratified epithelium of the gill arch and filaments. The difference in distribution of these leukocyte populations between the intestines and gills suggested a compartmentalisation of the mucosal immune system and the need to assess the immunological competence of mucosal tissues in Atlantic halibut.