The results on atmospheric deposition of heavy metals and other trace elements in Slovakia using the moss biomonitoring technique are presented. INAA at the IBR-2 reactor has made it possible to determine 38 elements in mosses collected in 2000 at 86 sampling sites. In addition to NAA, flame AAS (atomic absorption spectrometry) was applied to determine the content of S, Cd, Cu, Hg and Pb. The level of elements determined in bryophytes reflects the relative atmospheric deposition loads of the elements at the investigated sites. Factor analysis was applied to determine possible sources of trace element deposition in the Slovakian moss. The geographical distribution of factor scores and some element distribution maps over the investigated territory are presented. Both approaches aim at simplifying a complex interpretation of the results obtained due to the overlapping of different pollution sources and endemic zones such as in Brezová pod Bradlom in Malé Karpaty Mts. The marginal hot spots were revealed in Volovské Mts (Central Spiš), Kremnické and Štiavnické Mts (nonferrous ores processing and factories) and near dumps of stone chips (Slanec). The trans-boundary contamination by Hg through dry and wet deposition from Czech Republic and Poland is evident in the bordering territory in the north-western part of Slovakia (the Small Black Triangle), known for metallurgical works, coal processing and chemical industries. In comparison to the average Austrian and Czech values of heavy metal contents in moss, the Slovak atmospheric deposition loads of the elements were found to be 2–3 times higher on average.