The objective of this study was to evaluate the effect of L-arginine supplementation on the formation of jejunal lesions and micronuclei in Wistar rats following 5-fluorouracil (5-FU) treatment. Fifty rats were separated into five groups: CG served as the control group, GArg was supplemented L-arginine, G5-FU was administered 5-FU, GArg+5-FU was supplemented L-arginine/day and administered 5-FU, and Gciclo served as a positive control group for micronuclei formation. Jejunal lesions were assessed by histopathological analysis using a scoring system with a maximum of 39 points, based on the following lesions: lymph vessel dilatation, cubic enterocytes, villous flattening, villus fusion, interstitial edema, and apical necrosis of the villi. Micronuclei were counted in polychromatic erythrocytes from the femur bone marrow. The control and GArg rats had the lowest number of jejunal lesions (6.4 ± 2.8 and 5.3 ± 2.4, respectively) and micronuclei (1.9 ± 0.6 and 1.1 ± 0.3, respectively) while the G5-FU rats had the highest number of jejunal lesions (24.2 ± 4.9) and micronuclei (36.0 ± 8.5). The GArg+5-FU rats showed significantly reduced (P < 0.05) jejunal lesions (10.2 ± 4.9) and micronuclei (15.4 ± 5.9). In conclusion L-arginine supplementation potentially reduces the jejunal lesions and DNA damage caused by 5-FU.