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We studied the effect of heavy metal contaminations on genome instability of Chironomus annularius sensu Strenzke from three sampling sites on the River Chechło valley in southern Poland and a control site in Saraya, Bulgaria. The analysis of the heavy metal concentrations in sediments at the three river sites indicated concentrations higher than those in the fossil reference data (Zn 83-160 times, Pb 64-250 times, and Cd 210-793). According to the geoaccumulation index (Igeo), the sediments at all Chechło stations were classified as extremely polluted (Igeo class 6) by Cd, Pb and Zn while they were much less polluted by Cu (classes 1-3). The concentration of Cd, Pb and Zn in the sediments studied exceeded 21-79, 11-44 and 18-34 times the toxic effect threshold (TET) respectively; therefore, the sediments potentially have detrimental effects on the fauna. Genome instability was determined by somatic structural chromosome alterations (mainly heterozygous inversions) in the salivary gland chromosomes of C. annularius. On the basis of the number and frequency of these aberrations the somatic (S) and cytogenetic (C) indices were calculated as these indices allow a better quantification of the impact of heavy metals on organisms living in sediments. In the three Chechło sampling sites somatic aberrations occurred at a frequency significantly higher than in the control site (P<0.001). The three Chechło samples possess a high spectrum of somatic rearrangements with S index varying from 1.5 to 2.23 while in control site, S is 1.08. The C index of C. annularius from the polluted river sites varied from 0.163 to 0.380, far in excess of the C value of the control site (1.0), indicating strong pollution (<0.5) according to previous studies. In addition, a high level of inherited aberrations was detected (19 inherited band sequences, two of which were new). In all river stations the inverted homozygous band sequences A2.2 occurred in a high frequency (85%) and no standard sequences (A1.1) were observed. The transcription activity of Nucleolar Organizers (NORs) in chromosome arms A, C, E, G was often damaged and NOR activity was completely suppressed in 12.48% of larvae. Moreover, appearance of malformations in the external morphology of larvae was detected in 16.67% of larvae from all polluted sites. Therefore, the genome instability as estimated by two cytogenetic indices is a good biomarker of long-term toxicity and could be successfully implemented in the sediment monitoring procedures.