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Background and Objective: Several studies reported the immunological activity of Lycium barbarum. This study carried out to determine the effect of aqueous extract of fruits of Lycium ruthenicum L. on morphometric and histomorphometric indices in mice lymphatic organs. Methods: In this experimental study, 36 adult mice were randomly allocated into six experimental and control groups. The experimental groups were received Lycium ruthenicum L. fruit aqueous extract in the doses of 50, 100, 200, 400 and 800 mg/kg/bw, daily by feeding tube for 21 days. In the control group animals were recived 100 mg/kg/bw of saline using feeding tube. After the treatment, the relative increase in the body weight, morphometric, histomorphometric and histopathologic indices in thymus, lymph node and spleen were measured. Results: The administration of extract in doses of 50 and 100 mg/kg/bw did not effect on body weight of mice but in the doses of 200, 400 and 800 mg/kg/bw significantly reduced the body weight (P<0.05).Thymus index in 800 mg/kg/bw of extract significantly reduced in comparison with controls (P<0.05). Thickness of thymus medulla in low doses significantly increased while it was not visible in higher doses (P<0.05). Thickness of capsule in lymph node and spleen in dose of 800 mg/kg/bw significantly increased in comparison with control group (P<0.05). Low doses of the Lycium barbarum extract increased stimulation and infiltration of the immune cells and hematopoiesis in the lymphoid organs while in doses of 400 and 800 mg/kg/bw caused pathological changes including fibrosis in capsule, degeneration in follicles and stromal cell apoptosis. Conclusion: Aqueous extract of fruits of Lycium ruthenicum L. in doses of 400 and 800 mg/kg/bw causes histopathological alterations in the lymphoid organs.