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The dataset presented in this article supports “Selected persistent organic pollutants associated with the risk of primary ovarian insufficiency in women” (Pan et al., 2019). The supplementary data were as follows: (1) Detailed information regarding pretreatment methods, instrumental analysis and methods validation of quantification of serum concentrations of persistent organic pollutants (POPs). (2) The total dioxin equivalents (TEQs) levels of dioxin-like PCBs (DL-PCBs) in primary ovarian insufficiency (POI) cases and controls, as well as the association of TEQ levels with the risk of POI. (3) The results of principal components analyses (PCA) about 20 POPs that were detected in >40% samples. Keywords: Persistent organic pollutants, Polychlorinated biphenyls, Organochlorine pesticides, Primary ovarian insufficiency, Pretreatment methods