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Polychlorinated biphenyls (PCBs) are persistent environmental pollutants that are still causing potentially harmful effects to humans and wildlife. While the adverse health effects of PCBs have been extensively studied for decades, little is known about the effects specifically caused by the less potent, yet abundant non-dioxin-like congeners (NDL-PCBs). Here a non-targeted metabolic profiling of rat offspring exposed in utero and lactationally to total doses of 0, 300 or 1000 mg/kg body weight of ultrapure PCB 180 is reported. Serum samples from 5 male, and 5 female offspring from each group taken 12 weeks after birth were analyzed using UHPLC-qTOF-MS system, and subsequent metabolite alterations were studied. Statistical analysis revealed gender and dose-dependent alterations in serum metabolite levels at doses that did not adversely influence maternal or offspring body weight development. Male rats exhibited a higher number of altered metabolites, as well as stronger dose-dependency. A total of 51 metabolites were identified based on spectral matching. Most notably, 20 of these were glycerophospholipids, mainly lysophosphocholines with systematically decreased concentrations especially in the high-dose males. Other major metabolite groups include amino acids, their derivatives and carnitines. Our findings are consistent with the earlier reported liver effects, as well as neurodevelopmental and neurobehavioral effects of PCB 180. They also emphasize the potential value of metabolomics in characterizing toxic effects and in identifying sensitive biomarkers with potential future use in health risk assessment.Metabolome of rat offspring is affected by perinatal exposure to purified PCB-180.Effects are dependent on the dose by both quality, and magnitude.Male rats exhibit stronger effect on the metabolome than females.Role of non-dioxin-like congeners in environmental PCB mixtures is highlighted.Identified metabolites point to harmful effects on liver, and neurodevelopment.