Histopathological alterations in rainbow trout, Oncorhynchus mykiss, with 8.5 ± 0.2 g body weight subjected to acute and chronic paraquat exposure were studied by light microscopy. In experiment A, fish were distributed into four groups and exposed to 0 (group 1), 54 (group 2), 90 (group 3), and 150 (group 4) mg l-1 of paraquat for 96 h. In experiment B, fish were allocated into six groups and exposed to 0, 1.25, 2.5, 5, 10, and 20 mg l-1 of paraquat as groups 1 to 6, respectively, for 30 days. In experiment A, fish in group 2 showed cellular reduction in spleen white pulp, while in groups 3 and 4 other disorders such as hypocellularity and hyperemia in spleen red pulp were also shown. In all treatment groups, cellular reduction and sinusoidal blood congestion were observed in head kidney segments. In experiment B, fish spleen in higher doses of exposure (groups 5 and 6) showed signs of melanomacrophage accumulation while on day 30 lymphocyte reduction was also pronounced. In these groups, cellular density in pronephros also decreased on days 15 and 30 of exposure. According to the results of this study, it can be concluded that paraquat can affect spleen and head kidney tissues in acute and chronic exposure and these changes are directly proportionate to doses and duration of exposure. © 2012 Springer-Verlag London Limited.