The individual chromosomes in animal and plant interphase cell nuclei are discretely highly compartmentalized called “chromosome territories” that are visualized by 3D-FISH techniques. The chromosome territories are mutually exclusive without mixing each other, formed in essential components of the higher order chromatin architecture. Here I reviewed historical aspects of studies on the chromosome territory and recent advancement of studies on the chromosome positioning in relation to nuclear architecture. Chromosome positioning in the interphase cell nuclei has been investigated with regard to the following two aspects : radial positioning or relative positioning. It has been generally considered that the former radial positioning of a given chromosome territory is correlated with its size, its gene-density, and replication timing, namely comprehended as non-random distribution. From a series of 3D-FISH studies on the primate and chicken cell nuclei, the topology of the radial positioning of human chromosomes 18 and 19 homologs shows highly evolutionarily conserved during the evolution, but its functional significance is still within the speculation. On the other hand, the relative positioning has much affects to the translocation frequencies between adjacent two chromosomes, that was experimentally indicated by the mouse lymphoma cell nuclei, but in human lymphocytes the majority of reports suggested the random organization without particular patterns except for some clusters formed between homologous chromosomes. In future studies higher order nuclear architecture in relation to chromosome territory will be more elucidated by 3D-FISH techniques combined with living cell (in vivo) approaches by means of visualizing various nuclear molecules.