The study was designed to investigate the sub-lethal effects of paraquat on haematological parameters and histopathology of the gills, skin and liver of Clarias gariepinus juveniles of mean weight (38.26±1.20g) and length (17.50±1.55cm). The fish were exposed to 10, 20, 30, 40 and 50% of the 96hrsLC50 value of 107mg/l estimated from the 96 hours acute toxicity test. Blood samples were collected into heparinized tubes for the analyses of some haematological parameters, while the gills, skin and liver were also removed for histological examinations following standard procedures. The result revealed a significant reduction (P < 0.05) in the values of red blood cells (RBCs), haemoglobin (Hgb), packed cell volume (PCV) and erythrocytes indices from the control. The white blood cells (WBCs) and platelets (Plt) were however increasing significantly (P < 0.05) from those of the control as the test concentrations increased. The histology of the gills revealed some alterations such as epithelial proliferation, vacuolation of the mucus, hyperplasia of epithelial tissue of the gill filament, lifting and necrosis of the secondary lamellae. The exposed skin showed mucous cell proliferation, erosion of the epithelial lining, hypertrophy, necrosis of epithelial cells and widening of the epidermal and dermal layers. The liver exhibited cellular proliferation, sinusoid enlargement, congestion of the central vein, paranchymatous degeneration, vacuolar degeneration, pyknotic nucleic degeneration, legions and necrosis with severity as concentration of paraquat increases. The gills and skin were observed to be the most affected tissues in this study. The study also revealed that paraquat was toxic to C. gariepinus and causes some haematological and histopathological alterations in the fish blood and tissues at concentrations higher than 30mg/l. Therefore, the use of paraquat by farmers should be regulated particularly in area close to the aquatic environment.