Chromosome painting, utilizing tiling a path of bacterial artificial chromosome (BAC) clones, has been established for model plant Arabidopsis thaliana. This fluorescence in situ hybridization (FISH) method allows to identify individual chromosomes (or parts of these) in all cell cycle and developmental stages. Using chromosome painting, arrangement and potential dynamics of Arabidopsis interphase chromosome territories (CTs) were analyzed. Individual CTs were found to be associated at random frequency, except for the homologues of the nucleolar organizer region (NOR) chromosomes 2 and 4. Their higher-than-random association frequency was apparently mediatedt by attachment of NORs to a single nucleolus (in >90% of nuclei). The same arrangement was found in 2C, 4C and 8C nuclei isolated from roots and leaves. Somatic homologous pairing occurs in ~5% of Arabidopsis nuclei (i.e., not more often than expected at random). Thus, Arabidopsis differs from Drosophila (characterized by regular somatic pairing of homologues) and similarity in genome size, sequence organization and chromosome number does not necessarily cause an identical arrangement of interphase chromosomes. The lac operator/GFP-lac repressor tagging system is a powerful tool to study chromatin dynamics in vivo, however, it may not reflect the spatial chromatin organization at the integration loci under wild-type condition. FISH with lac operator and flanking endogenous sequences revealed that the transgenic tandem repetitive lac operator arrays pair with each other and associate with heterochromatic chromocenters significantly more often than average endogenous euchromatic regions do. The main reason is most likely the tandem repetitive nature of the transgene construct.