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Breast cancer is a common malignant tumor in women, and the anti-cancer effect of selenium (Se) is recognized. This meta-analysis was designed to determine the relationship between selenium levels in human tissue and breast cancer risk. Literatures published before August 2020 were systematically screened through PubMed, Web of Science, Scopus, and Elsevier. The related publication quality was evaluated by the Newcastle-Ottawa scale. We used random effect models for calculation and conducted sensitivity analysis and evaluation of publication bias. We identified 18 case-control studies, including 3374 women diagnosed with breast cancer and 3582 healthy controls. The results showed that the difference between the case group and the control group was - 0.53 μg/l [95%CI - 0.72 to - 0.34] (P < 0.001). Subgroup analysis showed a serum difference of - 1.14 μg/l [95%CI - 1.70 to - 0.58] (P < 0.001). The value of plasma was - 0.21 μg/l [95% CI - 0.37 to - 0.04] (P = 0.014). The value of toenail was - 0.21 μg/l [95% CI - 0.38 to - 0.03] (P = 0.021). In contrast, selenium levels in hair were not significantly associated with breast cancer risk. In the case-control studies, it was observed that selenium level in human tissues was negatively correlated with the risk of breast cancer, which may improve the understanding of the effects of selenium on human health.