SUMMARY. The family Chironomidae (non-biting midges) especially its larvae is a ubiquitous group of aquatic insects, very sensitive to contamination in the environment and changes in trophic status which make them suitable for ecotoxicological monitoring and risk assessment. Chironomid larvae are directly exposed to the contaminants and they are able to accumulate in their tissues different pollutants which later are transferred to fish and ducks and then to humans. Their genome is very sensitive to stress agents and it has a great potential in genotoxocological studies. They have excellent salivary gland chromosomes, which appeared to be promising tools to assess the genotoxicity in the environment. Due to their good resolution they provide the opportunity to detect a broad range of cytogenetic alterations at structural and functional level. Two types of structural alterations are considered: inherited affected whole individual and somatic, appeared in few cells of the individual. The chromosome rearrangements in Chronomids from Chernobil region after radiation are analyzed. The structural and functional alterations in the salivary gland chromosome in Chironomid from trace metal polluted stations are presented. The important key structures – Balbiani ring (BRs) and Nucleolar Оrganizer (NOR) in the polytene chromosomes are affected by trace metal toxicity and reduced their activity. The structural and facultative parts of the genome are considered. Most of somatic chromosome alterations are not randomly distributed: they occur more frequently in specific sites of the chromosomes composed either by satellite DNA or transposable elements. The genome alterations allow the species to be adapted in the stress agents in the environment and to preserve the species in these conditions. The analysis of cytogenetic response is potentially a powerful tool in preventing the long term effects of anthropogenic stress at population and community level.