Persistent organic pollutants (POPs) represent a concern for the environment and human health due to their persistence and toxicity. Exposure in Slovenia is geographically differentiated because the country, as part of former Yugoslavia, has a history of industry and regional contamination and is – at the same time – known for its clean nature. The PCB pollution of the Krupa River drew the public's attention to the chemical burden of Slovenians, and the demand for studies has been rising since. We assessed the exposure of men (n = 548) and primiparous women (n = 536) to POPs in 12 regions of Slovenia as well as exposure pathways via questionnaires. Most PCDD/Fs, PCBs, and PBDEs could be determined in pooled samples of maternal milk at low concentrations (1.57 pg/gTEQ, 1.47 pg/gTEQ, and 1076 pg/g fat, respectively), but a much lower number of compounds could be measured above the LOQ in pooled men's plasma samples (PCDD/Fs 0.08 pg/gTEQ, PCBs 0.007 pg/gTEQ, ΣPBDE 920 pg/g), and only HCB, p,p’-DDE, ΣDDT, and the non-dioxin-like PCB congeners 138, 153, and 180 could be determined in individual samples of milk (concentration range 5–60 ng/g fat). In individual samples of men's serum, only p,p’-DDE and ΣPCB were detected at concentrations of 0.25 ng/g and 0.3 ng/g, respectively. Nonetheless, we were able to differentiate between polluted and unpolluted areas on a national level, with higher exposure levels in the PCB polluted region of Bela Krajina, the industrial region Zasavje, and the capital, Ljubljana. Despite low concentrations, determinants of exposure, such as age, proximity to roads, old building materials, private water supplies, and consumption of alcohol, fish, meat, and eggs that have previously been observed only at higher levels could still be identified. Furthermore, levels of PCBs and PBDEs were highly correlated suggesting common exposure sources and pathways, whereas PCDD/Fs were correlated to a lesser extent. The calculated ratio between DDT and DDE in maternal milk samples was decreasing with the year of sampling, suggesting no ongoing exposure to DDT. The study findings suggest low exposure of men and lactating women to legacy pollutants in Slovenia, which gave rise to the hypothesis that Slovenia's geographical location might provide shelter from the long-range transport of POPs via Westerly winds. This hypothesis remains to be confirmed within future studies.