Genome editing using programmable nucleases has advanced significantly, enabling precise genetic modifications in eukaryotic cells. This review discusses current progress, future prospects, and challenges in developing nuclease-based therapies. Over 3,000 genes are linked to disease, and genome editing offers potential for treating monogenic disorders like severe combined immunodeficiency (SCID), haemophilia, and certain enzyme deficiencies. Existing therapies include gene therapy and RNA interference (RNAi), but they have limitations. Nuclease-based genome editing, such as using CRISPR-Cas9, offers the potential to correct mutations directly in affected cells. This technology can be used to introduce or correct mutations, insert therapeutic transgenes, or disrupt viral DNA. Genome editing can be applied through ex vivo or in vivo methods. Ex vivo approaches involve modifying cells outside the body and then re-introducing them, while in vivo approaches deliver nucleases directly to diseased cells. Both methods face challenges, including off-target effects, delivery efficiency, and immune responses. HDR is more precise than NHEJ but is limited to dividing cells. Improving HDR efficiency and specificity is crucial for clinical applications. Successful examples include using ZFNs to correct CCR5 mutations in HIV patients and gene correction in SCID-X1 patients. In vivo editing has shown promise in treating haemophilia and hereditary tyrosinemia. Challenges include ensuring safety, optimizing delivery systems, and reducing off-target effects. Non-viral delivery methods are being explored to minimize risks. Despite challenges, genome editing holds great potential for treating previously untreatable diseases. Regulatory and technological advancements are needed to ensure safe and effective clinical applications.Genome editing using programmable nucleases has advanced significantly, enabling precise genetic modifications in eukaryotic cells. This review discusses current progress, future prospects, and challenges in developing nuclease-based therapies. Over 3,000 genes are linked to disease, and genome editing offers potential for treating monogenic disorders like severe combined immunodeficiency (SCID), haemophilia, and certain enzyme deficiencies. Existing therapies include gene therapy and RNA interference (RNAi), but they have limitations. Nuclease-based genome editing, such as using CRISPR-Cas9, offers the potential to correct mutations directly in affected cells. This technology can be used to introduce or correct mutations, insert therapeutic transgenes, or disrupt viral DNA. Genome editing can be applied through ex vivo or in vivo methods. Ex vivo approaches involve modifying cells outside the body and then re-introducing them, while in vivo approaches deliver nucleases directly to diseased cells. Both methods face challenges, including off-target effects, delivery efficiency, and immune responses. HDR is more precise than NHEJ but is limited to dividing cells. Improving HDR efficiency and specificity is crucial for clinical applications. Successful examples include using ZFNs to correct CCR5 mutations in HIV patients and gene correction in SCID-X1 patients. In vivo editing has shown promise in treating haemophilia and hereditary tyrosinemia. Challenges include ensuring safety, optimizing delivery systems, and reducing off-target effects. Non-viral delivery methods are being explored to minimize risks. Despite challenges, genome editing holds great potential for treating previously untreatable diseases. Regulatory and technological advancements are needed to ensure safe and effective clinical applications.