Changes caused by microbial desulphurisation of low-maturity organic matter were investigated. Lignites and embedded sediments (R-r ca. 0.20-0.30%) with high organic matter content from the Belchatow, Turow and Kazimierz open cast mines (Poland) with variable mineral content and belonging to various lithotypes were desulphurised using Thiobacillus ferrooxidans and Thiobacillus thiooxidans. Extracts of crude (i.e. not desulphurised) and desulphurisated samples were separated into fractions of aliphatic, aromatic and polar compounds by preparative layer chromatography. Aromatic and aliphatic compound fractions were analysed by gas chromatography-mass spectrometry (GC-MS). There are several trends in changes in the composition of extracts that roughly correspond to results of biodegradation described for other types of organic matter like crude oils or bituminous coals such as significant decrease in the extract yields of desulphurised coals and a partial or total removal of several compound groups. Distributions and concentrations of n-alkanes are particularly changed, with short-chain compounds n-C-13-n-C-22 affected to the highest extent. Cyclic terpenoids, such as sesquiterpanes and diterpanes, were also removed, even from the xylithe extract composed in 90% of 16 alpha(H)-phyllocladane. Pentacyclic triterpanes distributions were not affected significantly, however their concentrations are lower in most of desulphurised samples than in the crude ones. Biodegradation accompanying desulphurisation shows much lower selectivity than that taking place in the nature. Despite the fact that aliphatic hydrocarbons were not removed from the extracts, aromatic hydrocarbons distributions are strongly affected, with total or partial naphthalene and phenanthrene derivatives removal. The values of geochemical indices are also affected by desulphurisation. The results indicate that microbial desulphurisation can significantly influence organic matter of lower maturity. Thus such changes should be taken into account when the process is considered to be applied in industry. (C) 2011 Elsevier Ltd. All rights reserved.