Molecular analyses have become an integral part of biomedical research as well as clinical medicine. The definition of the molecular and genetic basis of many human diseases has led not only to a better understanding of their pathogenesis, but has in addition offered new perspectives for their diagnosis, therapy, and prevention. Genetically, human diseases can be classified as monogenetic, complex genetic, and acquired genetic diseases. Based on this genetic classification, gene therapy involves four concepts: gene substitution, gene augmentation, block of gene expression or function as well as somatic transgene vaccination. Despite exciting recent developments, various delivery, targeting, and safety aspects need to be addressed before gene therapy will enter clinical practice. Clearly, molecular diagnosis and gene therapy of gastrointestinal diseases will be increasingly part of our patient management, complementing existing diagnostic, therapeutic, and preventive strategies.