The review summarizes modern views on to the structure and differentiation of the nuclear apparatus in ciliates. The genetic system of ciliates (type Ciliophora) includes two types of nuclei: germinal micronucleus (MIC) and somatic macronucleus (MAC). The MAC development is associated with the rearrangement of the MIC genome, which includes chromosome fragmentation and chromatin diminution. The loss of DNA constitutes from 10-15% (Tetrahymena termophila) to 95-98% of the genome in spirotrichs (Stylonychia, Oxytricha, and Euplotes). Analysis of molecular mechanisms underlying nuclear dualism in ciliates promoted radical revision of the concept on the interactions and roles of MAC and MIC. The micronucleus, as an inactive element, is an ideal field for the invasion and further expansion of mobile genetic elements. Chromatin diminution plays the purifying role, restoring the native genome structure. The process of recognition of "genetic garbage" to be eliminated has many features in common with the siRNA-mediated heterochromatization. The presence of this mechanism in very early radiated eukaryotic lineages (Opistokonta and Chromalveolata), indicates that it arose at the earliest stages of the eukaryotic evolution, probably, as a mechanism promoting genome integrity and stability.