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Data on concentrations of heavy metals (As, Cd, Cr, Cu, Fe, Hg, Mn, Ni, Pb, V and Zn) in moss collected on the lightly industrialized territory of Lithuania and on the highly industrialized territory of the Czech Republic in 1995, 2000 and 2005 is used to separate the background and anthropogenic contributions to heavy metal concentrations in moss. The distribution of the concentration logarithms allowed us to determine a background mode, and to estimate the background concentration of heavy metals from this mode. The method was then applied for an estimation of the contribution of local sources to the total pollution level in both countries. The average concentrations and the background modes of heavy metals in Lithuania and in the Czech Republic were very similar, except in the case of vanadium, where the background concentration was higher in Lithuania than in the Czech Republic. For most elements, the background concentration in moss had a decreasing tendency in Lithuania and in the Czech Republic between 1995 and 2005, though the concentration of Cu and Hg increased in Lithuania. The variability of chromium concentration in moss differed from the remaining investigated elements in the Czech Republic, and it was expressed as a bimodal lognormal distribution. This variability may be due to simultaneous contamination of moss by chromium from soil and from industrial sources of pollution.