Endoscopic treatment of gastrointestinal diseases has developed rapidly in recent years, due to its minimally invasive nature. One of the main contributing factors for this progress is the improvement of endoscopic instruments, which are essential for facilitating safe and effective endoscopic interventions. However, the slow learning curve required in the implementation of many advanced endoscopic procedures using standard devices is associated with a high risk of complications. Other routine procedures may also be complicated by unexpected difficulties. Based on the ferromagnetic properties of many objects, both internal and external magnetic devices have been developed and applied for multiple endoscopic interventions. The applications of magnets, mainly including compression, anchoring and traction, facilitate many difficult procedures and make it feasible to operate procedures that were previously impossible. Other novel endoscopic applications, such as magnetic nanoparticles, are also under development. In this article, we reviewed published studies of endoscopic applications of magnets for the treatment of gastrointestinal diseases such as precancerous lesions and cancer, obstruction, stricture, congenital and acquired malformations, motility disorders, and ingestion of foreign bodies. Since several endoscopic applications of magnets may also be relevant to surgery, we included them in this review.