Three-dimensional organization of genomes in every organism plays an essential role in regulating gene expression. Within the nucleus, chromatin is arranged in a hierarchical manner-forming compartments, topologically associating domains and chromatin loop structures—all of which contribute to gene expression control. Transposable elements, which are quite abundantly distributed within the eukaryotic genomes, seem to play decisive roles in optimizing the genome architecture. They often provide binding sites for various nuclear architectural proteins, which in turn influence chromosomal folding. Transposition events function at the level of chromatin compaction, loop formation, organization into topologically associating domains, and sequestration into chromosomal territories and often aid in the establishment and maintenance of centromeres. At the same time, transpositions in the context of the 3D genome can dynamically reorganize chromatin interactions and contribute to spatio-temporal regulation of gene expression patterns in response to developmental stages, environmental cues, or species-specific needs, ultimately driving evolution. Transposon-mediated alteration of chromatin structure has also been implicated in multiple diseases, including developmental abnormalities and cancers, thereby justifying the need for more extensive research in this field.