In this work, “Molecular Biology in Pediatric gastrointestinal and liver diseases”, the methods of molecular diagnosis which are applicable in the field of medicine were listed, showing their advantages and disadvantages, and as an example, their application on some gastrointestinal tract and liver diseases in children was related. Also, the methods of gene therapy, of which some are already applicable, and some are still under trails were listed, showing the application of each in the field of gastrointestinal and liver diseases in children. An imaginative idea of what will the management of disease is like with the full application of molecular diagnosis and gene therapy was shown.