The pathway followed by targeted gene repair is not fully elucidated. In its simplest iteration, the process is viewed as being initiated by the introduction of short (25–75 bases) synthetic single-stranded oligonucleotides into a mammalian cell. The oligonucleotide aligns in homologous register with the target gene using the underlying sequence complementarity as a guide. Once positioned properly, a single mismatched base pair is created between the oligonucleotide and the target site. The structural changes and altered DNA conformation that clearly take place during the pairing phase attract proteins involved in DNA repair pathway. Here we demonstrate the involvement of the homologous recombination (HR) process in gene repair. By using a phenotypic readout assay system, where an eGFP gene containing a single point mutation is integrated into DLD-1 cells, we observe between 0.7 and 1.5% correction of the mutation. Gene repair is assessed by FACS analyses, cell sorting and confirmatory DNA sequencing of the target gene. When the cells are arrested in S phase as a result of DNA damage incurred by the presence of hydroxyurea or thymidine, the level of gene repair increases 3 to 4 fold. Addition of the anticancer drug VP16 (etopside) or Camptothecin (CPT) induces a similar response for both episomal or chromosomal targets. Synchronized cells are also more amenable to the gene repair reaction once released into S phase and a synergistic effect is seen when cell synchronization is coupled to the addition of HU or thymidine or CPT. These results suggest that DNA damage at the replication fork stimulates the homologous recombination pathway to act upon strand lesions (double strand breaks, etc.), enabling a more efficient gene repair reaction to take place. Agents or enzymes that induce the double strand breaks repair response are also quite effective in regulating and elevating the frequency of gene repair. Taken together, we propose that the factors and/or protein activated by recombination induced by replication inhibition (RIRI), particularly those involved in HR, are capable of enhancing the frequency of gene repair in mammalian cells.