Medical system and methods are provided for forming an Anastomosis, such as an intestinal bypass anastomosis for treatment of obesity or diabetes. The medical devices and methods are minimally invasive and reduce complications. One embodiment of the method includes forming a first opening in the first section and forming a second opening in the first section. A proximal portion of the second section is moved to a position adjacent the first opening, and a distal portion of the second section is moved to a position adjacent the second opening. In this manner, an intermediate portion of the second section extends along the first section and an anastomosis can then be formed between the first section and the second section.