It is well known that an antagonistic effect exists between selenium (Se) and mercury (Hg), and that Se can play a protective role against Hg toxicity in organisms. In order to find an evidence for such connection, total Hg and Se were determined in 1654 umbilical cord blood samples, 1081 maternal blood samples, and 1051 breast milk samples in pregnant women from Slovenia, Croatia, Italy and Greece. Methyl mercury (MeHg) was determined in a subset of samples (468 umbilical cord blood samples, 364 maternal blood samples, and 268 breast milk samples). The study was part of a research project within the EU 6th framework programme Public health impact of long-term low-level mixed element exposure in susceptible population strata (PHIME). Total Hg and Se levels in cord blood of Slovenian women (Med 1.52 ng/g and 76 ng/g, respectively) were significantly lower compared to the levels in women from Croatia (Med 2.94 ng/g and 96 ng/g, respectively), Italy (Med 3.94 ng/g and 113 ng/g, respectively) and Greece (Med 5.81 ng/g and 104 ng/g, respectively). Total Hg levels in women from Greece were significantly higher than the levels in women from other countries, while the Se levels were the highest in women from Italy. Positive and significant linear correlation between Hg and Se was found in cord blood, maternal blood and breast milk of women in Slovenia, Croatia and Italy, while the association was poor and insignificant in women from Greece. Hg and Se were found to be associated also in blood of Slovenian women aged 50-59 and children aged 6-11 from mercury mine area, but not in children from other areas of Slovenia. Se in maternal and cord blood, but not in milk, was significantly correlated with the intake of many food items in pregnancy. The strongest direct associations regarded cheese and some vegetables (artichokes and fennels). In addition, both Hg and Se were significantly associated with fish consumption, possibly explaining correlations between these two elements found in selected biomarkers. Nevertheless, our observations might be also a consequence of a Se protective mechanism against mercury toxicity in certain populations.