Background: DNA-protein cross-links (DPCs) are a special type of DNA damage that is formed when a protein that participates in DNA transactions is irreversibly and covalently linked to DNA bases. DPCs are formed after exposure to chemicals, anticancer drugs, and ionizing radiation resulting in enzymatic and non-enzymatic DPCs. Up to now, the exact repair mechanism of DPCs has not been fully identified. Aim: The outputs of the current study provide molecular insights about the repair mechanism of enzymatic DPCs formed by DNA cytosine methyltransferase (DNMT). Materials & Methods: Cells were treated with 5-aza-2'-deoxycytidine (5-azadC) and the cytotoxicity, DNA damage and the role of essential DNA repair genes were examined. Results: A clear cytotoxic effect of 5-azadC was observed with LD₂₀ ranging from 0.4 to 5 µM. The analysis of DPCs by fluorescence labeling reveals that 5-azadC induces DPCs in a dose-dependent manner. Moreover, cells that are deficient in homologous recombination (HR) pathway (RAD51D and XRCC3) were 2-4 folds sensitive to 5-azadC compared to wild type. In contrast, cells deficient in nucleotide excision repair (NER) pathway (XPD and XPF) and Fanconi anemia (FANC) pathway (FancA, B, and C) were not sensitive.. Unexpectedly, mutation in nonhomologous end-joining (NHEJ) gene (DNA-PKcs) gives cells a great survival. Furthermore, double-strand breaks (DSBs) were significantly detected in HR mutant (RAD51D) compared with a wild type indicating that the replication fork stalled at the trapped DNMT site  generating DSBs. Conclusion: HR pathway genes (RAD51D and XRCC3) are essentially required for the repair of enzymatic-DPCs induced by 5-azadC and NER pathway genes have neglected roles. Further investigations are required to understand the accurate mechanism by which cells can repair DPCs that will provide good knowledge regarding the targeting of DPCs in cancer treatment.