Nuclear functions are strongly dependent on the three-dimensional organization of the interphase nucleus. Given the importance of telomeres in the behaviour and stability of chromosomes, we have investigated the architecture of the human nucleus from the telomere perspective by 3D-FISH and laser confocal microscopy. We observed a randomly scattered telomere distribution in all confocal sections of the interphase nuclear volume with various levels of telomere clustering in different cell types. This distribution is independent of H2AX presence or phosphorylation status. We also observed that telomeres usually cluster at the periphery of the nucleolus following its cell cycle dependent dynamic formation but are never present in the interior of the nucleolus. These perinucleolar telomeric clusters contain the telomeres of the short arms of acrocentric chromosomes, explaining the p-arm association of acrocentric chromosomes frequently found in metaphase. Thus, chromosome positioning in metaphase spreads is tightly connected to the three-dimensional architecture of the interphase nucleus. Copyright © 2008 S. Karger AG.