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Objective: To evaluate the antioxidant effect of quercetin on cell viability, reactive oxygen species (ROS) contents and apoptosis of cryopreserved mouse spermatogonial stem cells (mSSCs). Methods: mSSCs were isolated from neonate mice and cultivated in culture medium containing 30 μM quercetin for 48 h and then frozen for 2 weeks. After thawing, MTT assay was carried out to analyze the cell viability. Moreover, intracellular ROS levels were measured by flow cytometery and apoptosis was evaluated by detection of phosphatidylserine extalization assay and also real-time polymerase chain reaction. Results: Pre-treatment of mSSCs by 30 μM quercetin significantly decreased intracellular ROS content and apoptotic cell numbers and improved viability of mSSCs. Moreover, the gene expression of Bcl-2 and Bax significantly increased and decreased respectively after the freeze-thawing process. Conclusions: Pre-treatment of mSSCs with quercetin can improve cell viability and reduce apoptosis during freeze-thawing process. It can be a promising way to improve the quality and efficiency of cryopreservation protocols used in fertility preservation strategies.