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Gastric bypass surgery takes place in a hospital. Prior to the surgery, patients should follow all preparatory steps recommended by their physician. These may include modifications to diet, engaging in an exercise program and limiting or stopping use of alcohol and nicotine products. Patients may also be asked to refrain from taking certain medications, such as anticoagulants (e.g., aspirin) which inhibit the ability of the blood to clot. Fasting will also be necessary on the day of the procedure.

Patients are placed under general anesthesia, which means they are not awake for the procedure and feel no pain. A tube is inserted through the nose and into the upper stomach and connected to a suction machine, which will help in the healing process following surgery.

During the procedure, the stomach is made smaller by dividing it into a smaller upper section and a larger lower section. The surgeon uses surgical staples to seal off the upper part of the stomach from the remainder of the stomach. This creates a small pouch at the top of the stomach that is about the size of a walnut and is able to hold about 1 ounce (30 milliliters) of food.

The surgeon then cuts the small intestine and sews part of it onto the pouch. This arrangement allows food to bypass most of the stomach and the first section of the small intestine, known as the duodenum. Instead, the food travels from the surgically created pouch through the new connection (known as a Roux limb) and directly into the second segment of the small intestine, known as the jejunum. This limits the amount of calories absorbed into the body.

In rare cases, the gallbladder may also be removed (cholecystectomy) during a gastric bypass to prevent formation of gallstones that sometimes result from rapid weight loss. However, this is more often achieved through medications that dissolve these stones.

Gastric bypass surgery usually takes about four hours to complete. The incisions will be closed with stitches or surgical staples and then covered with a sterile bandage. The patient will have the stitches or staples removed at a later time during a follow up visit.