Replication timing is an important developmentally-regulated regional property that is correlated with chromosome structure and gene expression, but little is known about the establishment and maintenance of these patterns. Here we followed the fate of replication timing patterns in cells that undergo reprogramming either through somatic-cell nuclear transplantation (SCNT) or by the generation of induced pluripotential stem (iPS) cells. We have investigated three different paradigms, stage-specific replication timing, parental allele-specific asynchrony (imprinted regions) and random allelic asynchronous replication. In all cases, somatic replication timing patterns were reset exactly at the appropriate stage in early development and could be properly established upon re-differentiation. Taken together, these results suggest that unlike DNA methylation, the molecular mechanisms governing replication timing are not only stable, but can also be easily reprogrammed.