A fundamental difference between the somatic nuclei (macronuclei) of ciliates and the cell nuclei of higher eukaryotes is that the macronuclear genome is represented by a huge number (up to tens and hundreds of thousands) of “gene-sized” (0.5–25 kb) or “subchromosomal” (up to 2000 kb) minichromosomes. Electron microscopy data show that at the interphase stage, macronuclear chromatin usually looks like chromatin bodies or fibrils 200–300 nm thick. However, the question of how many DNA molecules are contained in an individual chromatin body remains open. In this work, we studied the ciliate Didinium nasutum and three species of Paramecium sp. The aim of the work was to clarify the organization of chromatin in macronuclei of ciliates differing in pulse-electrophoretic karyotype, and to what extent it corresponds to the model of topologically associated domains in the nuclei of higher eukaryotes. It was shown by the method of pulsed electrophoresis that the sizes macronuclear DNAs of the studied species are in the range of 50–1700 kb, but the majority of the molecules are less than 500 kb in length. A comparative quantitative analysis of pulse electrophoresis and electron microscopy data showed that at the stage of logarithmic growth of the culture, each chromatin body of P. multimicronucleatum contains one minichromosome, while the bodies in the macronucleus of D. nasutum contain two or more DNA molecules. However, during starvation when the activity of macronuclei decreased, chromatin bodies aggregated, which led to an increase in their size and/or the formation of 200–300 nm fibrils consisting of several chromatin bodies. A model for the formation of such structures is proposed. The data obtained show that, in terms of topological characteristics, chromatin bodies in the macronuclei with subchromosomal DNA molecules correspond to topologically associated domains of higher eukaryotes.