Purpose One of the most practical ways to utilise municipal solid waste is composting, thereby producing materials that may be productively used to improve soil properties. Wastes, as well as mature composts, contain hydrophobic substances, including fats, which are more resistant to microbiological decomposition than other constituents. The aim of this work was to determine qualitative and quantitative changes of hydrophobic substances, especially fatty acids, during the course of municipal solid waste composting. This provides new information on intensity of hydrophobic versus other substances decomposition undergoing during these processes. Materials and methods Raw materials, prepared according to MUT-DANO technology, were composted in a pile, and samples were taken after 1, 14, 28, 42, 56, 90 and 180 days of the composting. Temperature, moisture, total organic carbon, hydrophobic substances carbon (HSC) and fatty acid carbon (FAC) contents were determined in all samples. Hydrophobic substances were extracted with 1:2 (v/v) mixture of ethanol/benzene, while fats were extracted with petroleum ether and determined by GC analysis after transesterification with BF 3 in methanol.Results and discussion The HSC decreased from 27.8 to 9.3 g kg −1 during first 90 days of composting, and thereafter remained constant. Similarly, the highest content of FAC was in raw compost, while the lowest was after 90 days. Octadecenoic acid predominated in the raw compost and decreased from 56 to 23 % FAC after 180 days. During the composting processes, domination of octadecenoic acid was replaced by hexadecanoic and octadecanoic acids, which increased from 18.8 to 36.7 % and 8.3 to 19.4 % FAC, respectively. The share of hexadecanoic, eicosanoic and docosanoic acids increased after the thermophilic phase. The presence of odd-numbered fatty acids (pentadecanoic and heptadecanoic) was noted, which are known to be products of the bacterial transformation-synthesis of lipid substances. Conclusions The extent of decomposition of hydrophobic substances, especially fatty acids, is greater than other components in composted municipal solid waste, and intensity of the biotransformation is significantly correlated with composting parameters, mainly temperature and time. During the thermophilic phase of municipal solid waste composting, the decrease in total content of hydrophobic substances is approximately fivefold, while the reduction in fatty acids can be about tenfold. Unsaturated fatty acids are more intensively decomposed during the composting processes, while saturated fatty acids are more resistant. Moreover, transformation of fatty matter may result in the creation of specific isomers with odd numbers of carbon atoms.