► Detailed histological observations comparing the effects of Cu-NPs with CuSO4 in rainbow trout. ► Cu-NPs caused similar types of pathologies to CuSO4. ► There were material-type effects with Cu-NPs sometimes producing more injury. ► The first detailed observations on the trout brain injury for copper. ► Pathologies can occur indirectly without having elevated Cu in the internal organs. It is unclear whether copper nanoparticles are more toxic than traditional forms of dissolved copper. This study aimed to describe the pathologies in gill, gut, liver, kidney, brain and muscle of juvenile rainbow trout, Oncorhynchus mykiss, exposed in triplicate to either a control (no added Cu), 20 or 100μgl−1 of either dissolved Cu (as CuSO4) or Cu-NPs (mean primary particle size of 87±27nm) in a semi-static waterborne exposure regime. Fish were sampled at days 0, 4, and 10 for histology. All treatments caused organ injuries, and the kinds of pathologies observed with Cu-NPs were broadly of the same type as CuSO4 including: hyperplasia, aneurisms, and necrosis in the secondary lamellae of the gills; swelling of goblet cells, necrosis in the mucosa layer and vacuole formation in the gut; hepatitis-like injury and cells with pyknotic nuclei in the liver; damage to the epithelium of some renal tubules and increased Bowman's space in the kidney. In the brain, some mild changes were observed in the nerve cell bodies in the telencephalon, alteration in the thickness of the mesencephalon layers, and enlargement of blood vessel on the ventral surface of the cerebellum. Changes in the proportional area of muscle fibres were observed in skeletal muscle. Overall the data showed that pathology from CuSO4 and Cu-NPs were of similar types, but there were some material-type effects in the severity or incidence of injuries with Cu-NPs causing more injury in the intestine, liver and brain than the equivalent concentration of CuSO4 by the end of the experiment, but in the gill and muscle CuSO4 caused more pathology.