In the last decade, the number of bariatric surgery procedures increased dramatically in Israel similar to what has occurred worldwide. Bariatric surgery procedures have a proven efficacy in the treatment of morbid obesity. However, post-operative complications that involve the gastrointestinal tract may occur. Beyond the importance of early diagnosis and treatment, it is crucial to understand that we may decrease and prevent some of the complications by selecting the bariatric procedure according to the patient's medical background. This review addresses diagnosis, treatment and prevention of gastrointestinal diseases pre- and post-bariatric surgery procedures. Recommended pre-operative diagnostic procedures are listed including the eradication of helicobacter pylori and the protective effect of proton pump inhibitors. We reviewed the effect of specific bariatric procedures on gastroesophageal reflux disease and on intestinal motility. Prevention and treatment of nutritional deficits and metabolic complications are also discussed. Finally, this document was written by a panel of experts representing the attitudes of the Israeli Societies for Metabolic and Bariatric Surgery (ISMBS), Pharmaceutical (PSI), Study of Obesity and the Israeli Gastroenterology and Liver Diseases Association, all endorsed by the Institute for Quality in Medicine of the Israeli Medical Association (IMA).