Whole Exome Sequencing (WES) is a promising method in human genetics. Because the majority of pathogenic mutations that lead to the development of diseases are localized in exons and splice sites, WES could become a major tool for the diagnosis of diseases with a complex hereditary nature. This tool appears to be particularly useful for hereditary neurological diseases, such as autism spectrum disorders, Charcot—Marie—Tooth disease and others. In our review, we discuss the clinical application of WES, with special emphasis on the diagnosis of hereditary neurological diseases.