Abstract <p>Micronuclei are the extra-nuclear chromatin compartments separated from the primary nucleus and surrounded by their own nuclear envelope. For a long time, micronuclei were considered the final stage of the pathological processes in a cell. Therefore, they were exclusively used as biomarkers of the effects of genotoxic factors as well as of genome instability in various diseases. Presently, it has been demonstrated that micronuclei could be involved in the cellular activities, affect the nuclear genome, and lead to changes in the cell and tissue physiology. The formation of micronuclei is known to be one of the steps in selective chromatin elimination in the ontogenesis of particular plant and animal species. The regions to be marked and eliminated from cell nucleus are recognized at the level of the genome. This process is commonly accompanied by modifications with the heterochromatin formation, as well as changes in the chromosome condensation and in the position of chromosomes in the nucleus. The processes observed in selective and nonselective chromatin elimination are largely similar. The fact that the role of micronuclei in the cell functioning is yet to be understood and the composition of the micronuclei and the pathways of chromatin elimination can influence their role in the development of the pathogenesis emphasizes the importance of additional studies for profound understanding of this phenomenon.</p>