Individuals with rare diseases often face the challenges of long waiting periods for diagnosis and difficulty in accurate diagnosis. This process leads to a deterioration of the condition, causing a significant burden on individuals with rare diseases. To improve the diagnostic efficiency and accuracy of rare diseases, a variety of cutting-edge technologies led by high throughput next-generation sequencing technology have been introduced into the diagnosis of rare diseases, which not only deeply explore the genetic pathogenesis, and provide new ideas and directions for therapeutics and research.