High-throughput sequencing, also known as the high-throughput next generation sequencing (NGS), can sequence thousands of genes at one time, greatly improve the efficiency of DNA sequencing and reduce the cost. Recently, NGS has been widely used in medical research and clinical diagnosis. It has extensive applications in non-invasive prenatal screening, tumor screening, diagnosis and treatment, microbial pathogens detection, genetic diseases screening and diagnosis as well as organ transplantation rejection screening. However, as a new technology, NGS also has many issues in related clinical application. The quality management system is still imperfect and faces many challenges. Thus the joint efforts of medical laboratories and related departments are needed to promote the standardization of NGS in clinical diagnosis.