When it comes to their organisation, repetitive DNA sequences can be divided into dispersed repeats or transposons (retrotransposons and DNA transposons) and tandem repeats (microsatellite, minisatellite and satellite DNA). Segmental duplications are repetitive DNA sequences with both dispersed and tandem organzation. Due to their transmission mechanism, transposons introduce large number of mutations in genome. They can cause local gene instability and chromosomal rearrangements which affect genome organization. Microsatellite and minisatellite DNAs are unstable parts of eukaryotic genome and they evolve rapidly because they are places of frequent homologous recombination and DNA polymerase slippage during DNA replication. Satellite DNAs can be found in the pericentromeric, subtelomeric and interstitial regions of chromosomes and the centromeres and telomeres of chromosomes. They were once considered genomic junk, but today we know they have a role in the organization and function of telomeres and centromeres. Transncriptionally active satellite DNAs play an important role in gene expression and protein regulation. Homologous sequences in segmental duplications can result in non-allelic homologous recombination which causes chromosome rearrangements. Structural variations that occur as a result of segmental duplications create new genes that initiate evolution. Processes caused by repetitive DNA sequences participate in the evolution and organization of the genome in eukaryotes, and are described in more detail in this paper.