Long read sequencing (LRS) is emerging as a promising tool for the routine diagnosis of genetic diseases. Traditional genetic testing methods, such as short-read sequencing (SRS), have limitations in detecting structural variants (SVs), repeat expansions, and other complex genomic regions due to their inability to accurately map repetitive or GC-rich sequences. LRS, which generates longer reads with improved mappability, is more suitable for detecting these challenging genomic regions. While LRS is not yet widely available in clinical settings, it has shown potential to enhance diagnostic yield and reduce reporting times by enabling the detection of SVs, repeat expansions, and other complex variants that are difficult to identify with SRS. LRS can also be used for single nucleotide variant (SNV) detection, particularly in genes with highly homologous pseudogenes, and for haplotype reconstruction to assess the parental origin of pathogenic variants. LRS has been successfully applied in the diagnosis of various genetic disorders, including structural variants, tandem repeats, and complex SVs. It has demonstrated the ability to detect SVs that are missed by SRS, such as large deletions, inversions, and complex rearrangements. In cases of autosomal recessive diseases, LRS can resolve haplotype phasing, helping to determine the genetic diagnosis in compound heterozygote cases. Additionally, LRS has been used to identify pathogenic variants in genes with high homology to pseudogenes, such as PKD1 and CYP21A2, improving the accuracy of diagnosis. LRS also has potential in the detection of methylation changes at imprinted genomic regions, which are important in imprinting disorders. While methylation analysis is currently more focused on identifying defects responsible for imprinting disorders, LRS can simultaneously detect both DNA sequence alterations and base modifications, providing a more comprehensive diagnostic approach. Despite its potential, LRS is not yet a first-tier diagnostic test due to technical limitations, including high costs and the need for advanced bioinformatic tools. However, ongoing technological advancements are expected to improve the accuracy and efficiency of LRS, making it a valuable tool for the diagnosis of genetic diseases in the future.Long read sequencing (LRS) is emerging as a promising tool for the routine diagnosis of genetic diseases. Traditional genetic testing methods, such as short-read sequencing (SRS), have limitations in detecting structural variants (SVs), repeat expansions, and other complex genomic regions due to their inability to accurately map repetitive or GC-rich sequences. LRS, which generates longer reads with improved mappability, is more suitable for detecting these challenging genomic regions. While LRS is not yet widely available in clinical settings, it has shown potential to enhance diagnostic yield and reduce reporting times by enabling the detection of SVs, repeat expansions, and other complex variants that are difficult to identify with SRS. LRS can also be used for single nucleotide variant (SNV) detection, particularly in genes with highly homologous pseudogenes, and for haplotype reconstruction to assess the parental origin of pathogenic variants. LRS has been successfully applied in the diagnosis of various genetic disorders, including structural variants, tandem repeats, and complex SVs. It has demonstrated the ability to detect SVs that are missed by SRS, such as large deletions, inversions, and complex rearrangements. In cases of autosomal recessive diseases, LRS can resolve haplotype phasing, helping to determine the genetic diagnosis in compound heterozygote cases. Additionally, LRS has been used to identify pathogenic variants in genes with high homology to pseudogenes, such as PKD1 and CYP21A2, improving the accuracy of diagnosis. LRS also has potential in the detection of methylation changes at imprinted genomic regions, which are important in imprinting disorders. While methylation analysis is currently more focused on identifying defects responsible for imprinting disorders, LRS can simultaneously detect both DNA sequence alterations and base modifications, providing a more comprehensive diagnostic approach. Despite its potential, LRS is not yet a first-tier diagnostic test due to technical limitations, including high costs and the need for advanced bioinformatic tools. However, ongoing technological advancements are expected to improve the accuracy and efficiency of LRS, making it a valuable tool for the diagnosis of genetic diseases in the future.