Abstract: Background and Objective: The use of phytoadditives in fish culture is on the rise due to their greater advantages over the synthetics drugs. Moringa oleifera saponins has a positive effect on fish growth, however little is known about its effects on liver and intestine. Thus, this study was aimed at investigating the effects of crude extract of Moringa oleifera saponin on liver and intestine histology of Clarias gariepinus. Materials and Methods: Crude saponins were isolated from Moringa oleifera leaf using standard procedures. Two hundred and forty fish divided into 4 groups (A, B, C and D) and fed for 60 days with varying concentrations of the crude extract (0.0, 0.5, 1.0 and 1.5 g kg–1) incorporated into basal diet. At the end of the study, liver and intestines from fish in each group were sectioned using standard procedure. Results: Photomicrograph impression of the fish liver in the control group revealed normal central vein and fats cells. While in the other groups deposit of fat cells distorting the normal architecture of the liver and fibrosis were observed as the concentration of saponin increases. The intestine of fish in the control group revealed normal mucosal lining. While in the other groups normal mucosal lining and gradual increase in the number of inflammatory cells in submucosa were observed as the concentration of saponins increases. Conclusion: This study infers that crude extract of Moringa oleifera saponins affects the structure of the liver and causes inflammation in the intestine of Clarias gariepinus especially at high concentrations.