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Fluorescence in situ hybridization with centromeric, telomeric and whole chromosome paint probes was used to study nuclear topology in epididymal sperm as well as spermatids from testis tissue sections of the rat. Pericentromeric regions of 9 chromosomes of the rat (n=21) were labeled with a satellite I specific DNA probe. Pericentromeres showed few tandem associations in spermatids of steps 1-8 of spermiogenesis. At step 9, pericentromeric regions associated to form an elongated cluster in the spermatid nucleus. This arrangement was also seen in the sperm nucleus. FISH with telomere probes revealed numerous, variably arranged signals in round and elongated spermatids as well as sperm nuclei. Telomere signals showed a tendency for pairwise association which was more pronounced in elongated spermatid and epididymal sperm nuclei. FISH to DTT treated sperm suggested that telomeres reside at the periphery and that pericentromeres are located in the nuclear interior. Chromosome painting with rat chromosome 2 and 12 specific microdissection library probes showed that these chromosomes predominantly occupy compact and variably shaped territories during spermatid maturation. In elongated epididymal sperm nuclei chromosome 2 and 12 territories took up specific positions. We suppose that the associations of pericentromeres during step 9 render a well defined nuclear topology which facilitates the ordered compaction of the genome at subsequent stages.