Study of comparative genomics has revealed that about 5% of the human genome are under purifying selection, 3.5% of which are conserved non-coding elements (CNEs). While the coding regions comprise of only a small part. In human, the CNEs are functionally important, which may be associated with the process of the establishment and maintain of chromatin architecture, transcription regulation, and pre-mRNA processing. They are also related to ontogeny of mammals and human diseases. This review outlined the identification, functional significance, evolutionary origin, and effects on human genetic defects of the CNEs.