Orderly replication of DNA is a prerequisite to the faithful segregation of the chromosomes before cell division. These processes occur in an environment where the natural order of events can be perturbed by DNA damage, which may in turn cause the replication fork to stall or even break down. Such events can trigger cellular checkpoints, which allow time for repair of damage before replication resumes. It is interesting that replication pausing can also occur naturally and that pausing and specific pause sites have been conserved throughout evolution in both prokaryotes and eukaryotes. Although it appears that these sites are important for the regulation of replication termination and to prevent collisions between the replication and transcription machinery, there is no definitive evidence as to their precise function. In this review we consider replication pausing in prokaryotes and eukaryotes. We distinguish between replication blocks and pause sites as well as programmed versus accidental pausing. We also discuss how pausing can lead to increased recombination.