Structural characteristics and polymorphism of long (LNR) and short (SNR) mitochondrial non-coding regions of the liver fluke Fasciola hepatica were studied. The flukes were obtained from several populations of Russia and Belarus. The amplification of LNR yielded a set of 10 fragments with the length of neighbouring ones differing in one tandem repeat (85 bp; published earlier for Australian fluke). LNR amplification fragments of different length were cloned and sequenced. Comparison of the LNR sequences of Australian and Belarussian flukes revealed 3 nucleotide substitutions and one point heteroplasmy of the first nucleotides in the imperfect repeat and four adjacent perfect repeats. Positions of the three mutations coincide in perfect and imperfect repeats and the frequency of mutations is 4-4.7% while the frequency of heteroplasmic sites varies from 0.1 to 1.2%. It was shown that the presence of mutations and the heteroplasmy of one site can change the structure and stability of the putative secondary structures of the perfect and imperfect re- peats. The amplification of SNR of F. hepatica from several populations yielded fragments which differed from the published SNR sequence of Australian F. hepatica in the single transversion. Both non-coding regions have several conservative and potentially regulatory sequences. Probable cause of heteroplasmy and concerted origin of substitutions in different repeats are discussed.