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Persistent organic pollutants (POPs) accumulate in the organisms due to their hydrophobicity and resistance to xenobiotic metabolism. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is one of most representative POPs. Its pathophysiological effects have been extensively studied on many types of tissues but not on muscles. In this study, female C57BL/6J mouse model was used to analyze the long-term effects of maternal exposure to TCDD during gestation and lactation on the skeletal muscles (soleus, plantaris, and gastrocnemius) of the progeny during adulthood. The effects of re-exposure to TCDD in mice exposed during their development were also characterized. Female C57BL/6J mice were maternally exposed to TCDD or its vehicle (n-nonane in corn oil) and then re-exposed to TCDD or its vehicle at 9 weeks of age. The metabolites in the skeletal muscles were analyzed by gas chromatography–quadrupole time of flight-mass spectrometry (GC–qTOF-MS). Univariate analysis showed significant effects in certain metabolites in the skeletal muscle. It also showed that TCDD exerts a more significant impact on exposure to TCDD at 9 weeks of age than during maternal exposure for the soleus. On the other hand, TCDD exerts a more significant impact on mice maternally exposed to TCDD than at 9 weeks of age for the gastrocnemius. Multivariate analysis showed clear discrimination between the TCDD-exposed mice and the control. This study demonstrates the effects of TCDD observed following maternal exposure; some of them can be reinforced or attenuated by a re-exposure at the adult age, suggesting that the POP which mainly acts through the activation of the AhR leads to metabolic adaptation in the skeletal muscles. The period of exposure was a key factor in our study with TCDD playing a crucial role during the maternal period, as compared to when they were exposed at 9 weeks of age. It was inferred that disruption in amino acid metabolism might lead to a loss in muscle mass which may result in muscular atrophy. Our results also show that the metabolite profiles after perinatal exposure are different in different types of muscles even though they are all classified as skeletal muscles. Therefore, TCDD may affect the organism (specifically different skeletal muscles) in a non-homogenous manner.