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1)Background: Kidney stones is one of the serious medical conditions affecting populations worldwide. So, we aimed in this study to investigate the protective effect of allium cepa administration against KSD. 2)Methods: 24 adult male albino rats were assigned into 3 groups; group I: control group; group II: received ethylene glycol (EG) in the drinking water for 4 weeks; and group III received EG in the drinking water plus freshly prepared allium cepa extract (ACE) for 4 weeks. Renal function tests and urine analysis were done. Tissue oxidative stress markers (SOD and MDA) were assessed, and kidney expression of SIRT-1, Beclin, LC3, osteopontin, and Regucalcin were measured by RT-qPCR. Histopathological assessment and immunohistochemistry for Bax, Beclin-1 and TNF-α were performed. 3)Results: There was a significant improved kidney function tests in the ACE received group compared to EG group (P < 0.001). The present study showed less stones formation and apoptosis with decreased osteopontin and autophagy genes expression in the ACE received group compared to EG group (P < 0.001). While, regucalcin and SIRT-1 genes showed higher expression in the former group than the later group (P < 0.001). 4) Conclusion: Alium Cepa extract administration has a significant protective effect against kidney stones formation.