Chromosome-specific paints and in situ hybridization have revealed that chromosomes are highly organized and compartmentalized within somatic nuclei, an arrangement that may affect the control and modification of the genome. Now, on p. 1811, Joanna Bridger and colleagues report that the chromosomes in sperm nuclei are also non-randomly positioned and that the sex chromosomes reposition during late spermatogenesis. The authors describe the longitudinal and radial position of all the chromosomes in spermatocytes and spermatids in three breeds of pig. Most interestingly, they find that, as in somatic cells, the sex chromosomes are at the nuclear edge in primary spermatocytes but, in spermatids, these chromosomes are more centrally located. Consequently, they must be among the last chromosomes to be affected by the maternal cytoplasmic environment after fertilization. The authors suggest that the non-random positioning of the chromosomes in sperm determines when particular chromosome regions are remodelled after fertilization. This could allow some degree of epigenetic control over paternal gene expression in the embryo.