Localization, as detected by in situ hybridization, of major heterochromatic blocks in interphase nuclei of larval brain and imaginal discs is reported. We conclude that the position of heterochromatic regions in interphase nuclei is correlated with their respective position in metaphase chromosomes and hence, independent of sequence recognition. Furthermore, chromocentral associations of X-, Y- or autosomal-based heterochromatin are not formed in these cells. Homologues do align in close proximity, but heterochromatin plays no role in this arrangement. Heterochromatin, and probably nucleoli, establish their membrane links in situ, and have no prefixed recognition sites. The most intimate association between homologous repetitive sequences was found in the histone locus, but no tendency for clustering was found among loci of multisite euchromatic gene families.