In the course of development, both endogenous and exogenous factors can cause DNA damage, which resulted in somatic mutations. It is recongnized that somatic mutations are the causation of many nervous cancers, the pathogenicity of somatic mutation in developmental malformation of nervous system is unknown yet. With the development of next generation sequencing (NGS), especially the clinical application of the whole-exome sequencing and the targeted massively parallel sequencing, the somatic mutations with low levels can be detected precisely. The detection of low-level and tissue-specific somatic mutation in patients enables researchers to re-recognize the contribution of somatic mutation to neurological disorders. In this review, we systematically summarize the pathogenicity and characteristics of the somatic mutations in the common tumors and developmental malformation of nervous system, and the new technologies to detect somatic mutation in order to extend our understanding of its genetic etiologies and identifying the new drug targets in the future.