In the last decade, with the advent of next generation sequencing (NGS), sequencing of genes and diagnosis of genetic disorders have entered a new realm. Using this technology, it has been possible to identify the genetic cause of many diseases and syndromes such as congenital disorders and malformations which previously were considered as “with unknown causes”. NGS technology consists of several methods including genome preparation and fragmentation, sequencing, visualization and data analysis. Some of the important applications of NGS technique include: diagnosis of genetic diseases with multiple disease causing gene, preimplantation genetic diagnosis, pharmacogenomics, epigenetics and identification of structural variations in the genome. In this study, this technology was introduced and its increasing application in molecular diagnosis of genetic diseases was briefly discussed.