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Little information is available on exposure of general population to metals at low levels. As a part of a research project PHIME within the EU 6th Framework programme and National Human Biomonitoring programme, several studies following the same protocol were conducted to find out to what extent the Slovenian population of women in childbearing age, women 50–60 years, men and children 6–11 years is exposed to environmental chemicals including Hg, Pb, Cd and As and on the other hand to estimate their supply with essential elements (Se, Zn, Cu). Hair, blood and urine were collected from all participants, breast milk from lactating mothers. Most of the subjects had the levels for non-essential toxic metals below the reference levels and the levels for essential elements Zn, Cu and Se within the reference intervals. Concentrations of metals and As did not differ between genders, while significantly higher levels of Se were observed in men and significantly higher levels of Cu in women. Comparing women of different ages, higher Hg levels and lower Cd and Pb levels were found in blood of younger women (20–35) than in older women (50–60). Se levels were higher in older women, while Cu and Zn levels were higher in younger women. In compare to children, women (both, younger and older) and men showed higher Cd, Pb, Se and Zn concentration in blood. Hg concentration was higher in women (20–35) and men than in children. Looking at the difference between different geographical areas where subjects were recruited, we found higher Cd and Pb levels in blood of rural children than in children from urban area. Hg in blood and urine was in contrary, higher in children from urban area than in children from rural area. In adults, As was observed to be the highest in urban area. Levels of essential elements differed between different areas in Slovenia as well. The present study has provided the basis to establish preliminary reference values for the selected population, depending on different parameters assessed by questionnaires. When additional subjects from other areas of Slovenia are recruited, the connection to the environmental database will be established using GIS modelling tools.