Although early replication has long been associated with accessible chromatin, replication timing is not included in most discussions of epigenetic marks. This is partly due to a lack of understanding of the mechanisms behind this association but the issue has also been confounded by studies concluding that there are very few changes in replication timing during development. Recently, the first genome-wide study of replication timing during the course of differentiation revealed extensive changes that were strongly associated with changes in transcriptional activity and subnuclear organization. Domains of temporally coordinate replication delineate discrete units of chromosome structure and function that are characteristic of particular differentiation states. Hence, although we are still a long way from understanding the functional significance of replication timing, it is clear that replication timing is a distinct epigenetic signature of cell differentiation state.