Replication foci are the units of DNA replication in the nucleus. They harbor the replication machinery and active replicons. Spooling of individual replicons appears to occur at replication foci of budding yeast. The dynamics associated with fork progression in mammalian nuclei are largely unclear but large-scale spooling of DNA does not occur. Replication foci are arranged into spatio-temporal higher-order patterns. Different kinds of such patterns have been observed in different eukaryotic taxa but the characteristic patterns observed in mammals are highly conserved. The changes of higher-order patterns of replication foci during S phase progression are in mammals due to the sequential association of the replication machinery with neighboring stably positioned chromatin domains, which leads to the sequential formation of replication foci at neighboring nuclear sites. These findings suggest that the spatio-temporal patterns of replication foci are determined by the underlying genome architecture. Future studies will have to address the question in which way exactly genome architecture is involved in the spatial and temporal regulation of DNA replication.