A study on the microbial diversity in two uranium mine waste heaps revealed that many different physiological groups of microorganisms occurred. The acidophilic thiobacilli Thiobacillus ferrooxidans and Thiobacillus thiooxidans were the dominant microorganisms in a uranium mine waste heap with a mean pH-value of 4. Moderately acidophilic thiobacilli dominated in a second heap with carbonaceous material and a mean pH-value of 6. Tetra- and pentathionate were detected in carbonaceous ore samples, Polythionates are the main products in the case of chemical pyrite oxidation experiments at pH 7.9, explaining the source of substrate for the moderately acidophilic thiobacilli. In the case of pyrite oxidation at pH 1.9 more than 90 % of the pyritic sulfur was completely oxidized to sulfate, together with 10 % of elemental sulfur and traces of polythionates. Elemental sulfur is a suitable substrate for Thiobacillus thiooxidans. For remediation purposes the action of inhibitory substances on bacterial leaching was tested. An efficient inhibition of the acidophilic leaching bacteria Thiobacillus ferrooxidans, Thiobacillus thiooxidans, and Leptospirillum ferrooxidans was achieved by sodium dodecylsulfate (SDS), calcium fluoride (CaF2), concrete, and limestone (CaCO3). The latter three agents were suitable for a long-term protection of mine waste resulting from measurements of microbial activity, cell count, and metal solubilization. Dissolved SDS allows for a temporary treatment.