Abstract We investigated the potential endocrine disruptive effect of prenatal exposure to persistent organic pollutants (POPs) through maternal diet, by measuring anogenital distance in newborns and young children. We included 231 mothers and their newborns measured at birth from the Rhea study in Crete, Greece and the Hmar study in Barcelona, Spain and 476 mothers and their children measured between 1 and 2years from the Rhea study. We used food frequency questionnaires to assess maternal diet and estimated plasma dioxin-like activity by the Dioxin-Responsive Chemically Activated LUciferase eXpression (DR-CALUX®) and other POPs in maternal samples. We defined a “high-fat diet” score, as a prenatal exposure estimate, that incorporated intakes of red meat, processed meat, fatty fish, seafood, eggs and high-fat dairy products during pregnancy. Increasing maternal “high-fat diet” score was related to increasing dioxin-like activity and serum concentrations of lipophilic persistent organic pollutants in maternal blood. An inverse dose–response association was found between “high-fat diet” score and anoscrotal distance in newborn males. The highest tertile of the maternal score was associated with −4.2mm (95% CI −6.6 to −1.8) reduction in anoscrotal distance of newborn males, compared to the lowest tertile. A weak positive association was found between the “high-fat diet” score and anofourchetal distance in newborn females. In young children we found no association between maternal “high-fat diet” score and anogenital distances. In conclusion, maternal high-fat diet may be linked to high prenatal exposure to persistent organic pollutants and endocrine disruptive effects, resulting to phenotypic alterations of the reproductive system.