Cost of feed is threatening sustainability of aquaculture, use of non-conventional feed ingredients is becoming necessary, but their effects on both humans and animal health are equally important. The present study investigated the effects of processed moringa seed kernels (MSK) (raw, toasted, boiled, autoclaved and ethanol soaked) on the histology of Clarias gariepinus fingerlings. The experimental fish were fed processed MSK diets at levels of 0%, 25%, 50%, 75% and 100% respectively. Plastic bowls of thirty five litres were used for fifty six days feeding trials, twenty fish were stocked in completely randomize designed. The experimental fish with average weight of 2.50g were used. The findings of this study indicated that Clarias gariepinus fingerlings could tolerate up to 50% inclusion level of boiled MSK without any negative effect. It can also be concluded that raw, ethanol soaking, toasting and autoclaving of MSK can cause structural abnormalities in the histological organs (liver and kidney) resulting in severe physiological problems. These conditions can cause even death of the fish. It is therefore recommended to use boiled MSK at 50% inclusion level when use in aquaculture to maintain healthy conditions for the better survival of fishes.