In eukaryotic cell nuclei the genome is organized into large loops attached to the nuclear matrix. Rearrangements of the genome frequently occur via an illegitimate recombination between loop anchorage sites resulting in deletion or repositioning of DNA loops. The illegitimate recombination between loop anchorage sites is possibly mediated by topoisomerase II. Treatments stabilizing intermediate covalent complexes of topoisomerase II with DNA seem to increase the possibility of illegitimate recombination between loop anchorage regions. On the basis of these and some other observations we suggest that chromosomal DNA loops constitute basic units of the genome evolution, or, in other words, structural blocks of the eukaryotic genome.