We have analyzed the spatial and temporal relationship between transcription and replication sites during the first cell cycle in mouse embryos. Embryos were microinjected with both 5-bromouridine-5'-triphosphate and digoxygenin-11-deoxyuridine-5'-triphosphate to visualize transcription and replication sites respectively. We detected six different phases of replication during S phase and dated the onset of zygotic transcription at the end of the S phase. Using confocal microscopy, we showed that there is essentially no colocalization of replication and transcription sites at this stage of development. Moreover, studies on aphidicolin-treated embryos demonstrated that inhibition of DNA replication does not hinder transcriptional activation at the 1-cell stage.