Perfluorinated chemicals (PFCs) form a special category of organofluorine compounds with particularly useful and unique properties. Their large use over the past decades increased the interest in the study of their environmental fate. Fluorocarbons may have direct or indirect environmental impact through the products of their decomposition in the environment. It is a common knowledge that biodegradation is restricted within non-perfluorinated part of molecules: however, a number of studies showed that defluorination can readily occur during biotransformation. To evaluate the fate of PFCs in the environment a set of principal transformations was developed and implemented in the simulator of microbial degradation using the catabolite software engine (CATABOL). The simulator was used to generate metabolic pathways for 171 perfluorinated substances on Canada's domestic substances list. It was found that although the extent of biodegradation of parent compounds could reach 60%, persistent metabolites could be formed in significant quantities. During the microbial degradation a trend was observed where PFCs are transformed to more bioaccumulative and more toxic products. Perfluorooctanoic acid and perfluorooctanesulfonate were predicted to be the persistent biodegradation products of 17 and 27% of the perfluorinated sulphonic acid and carboxylic acid containing compounds, respectively.