Endogenous retroviruses (ERVs) are genetic elements derived from a process of germline infection by exogenous retroviruses. Some ERVs have been co-opted for physiological functions, and their activation has been associated with complex diseases, including Autism Spectrum Disorder (ASD). We have already demonstrated an abnormal expression of ERVs in the BTBR T + tf/J (BTBR) mouse model of ASD during intrauterine life till adulthood. Thus, starting from the assumptions that ERVs may contribute to the derailment of neurodevelopment and that ASD has fetal origins as a consequence of adverse intrauterine conditions, the present study aims to characterize the transcriptional activity of selected ERVs (MusD, IAP, Syn-A, Syn-B, ARC and GLN), LINE-1, inflammatory mediators (IL-6, IL-10, IL-11 CXCL-1) at the maternal-fetal interface and in dissected embryos from BTBR mice. Our results highlight the deregulation of ERVs and inflammatory mediators at the maternal-fetal interface, and in cephalic and non-cephalic embryonic tissues from BTBR compared to C57BL/6 J. Several correlations among ERV expression levels emerged in different tissues from C57BL/6 J mice while, in BTBR mice, no correlations were found, suggesting that in this model, the acquisition of autistic-like traits might be linked to the dysregulation of ERV activity occurring during intra-uterine life.