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The within-site correlations between soil respiration rates, lead (Pb), mercury (Hg) and cadmium (Cd) concentrations and organic matter quality variables were investigated at four sites in southern Sweden. The aim was to study whether the within-site variation in heavy metal concentrations could be used to monitor biological effects of regional deposition of heavy metals. Two sites in the south-west, one in the mid-south of the country, and one in south-east were investigated. At the south-eastern, least contaminated, site there were no correlations between soil respiration rate, and either organic matter quality variables or heavy metal concentrations. At the remaining sites, negative correlations were found between Pb and soil respiration rate. However, at two of these three sites there was a covariation with cellulose that could account for these correlations. The within-site variation of pH and total nitrogen (N) was low, and did not show any correlative general trends with either respiration rate or heavy metals. Meta analysis showed that negative correlations between Pb or Hg, on the one hand, and cellulose or hemicellulose on the other were generally found in within-site investigations. However, this does not necessarily explain the correlation between Pb and soil respiration, as was shown for the southernmost site. A PLS model of soil respiration rates at this site, using all measured variables, including heavy metals, explained more variation than a model developed using only mor layer thickness, pH, carbohydrate, ash and nitrogen concentrations, as independent variables. Thus there is a risk of toxic effects from Pb even at the levels found in south-western Sweden today (>120 μg Pb * g dw−1). However, since the correlations between heavy metals and cellulose were not significantly different at the different sites, random sampling variation could not be ruled out as an explanation of the different results for the different sites. The causes of the correlation between organic matter quality and heavy metals have not yet been clarified. Analysis of mor samples incubated in the laboratory for 2 yr with 1200 μg Pb * g dw−1 or 5 μg Hg * g dw−1 did not show any differences in carbohydrate composition, compared to control samples. This shows that within-site studies of correlations between respiration rate and heavy metals have to be combined with studies of metal additions to soils and analysis of organic matter quality before any valid conclusions can be made.