Method for treating a Roux-en-Y patient having fistulas and leaks as a result of bariatric surgery. A gastrointestinal implant device is anchored in the esophagus and extends through a stomach pouch into an intestine anastomosed to the stomach pouch to prevent fistulas and other damaged tissue from making contact with food and fluids entering the esophagus. The gastrointestinal implant device includes an unsupported flexible sleeve and an anchor coupled to a proximal portion of the sleeve. The flexible sleeve is open at both ends, and adapted to extend below a jejunum. The anchor is adapted to be retained within the esophagus, preferably just above the gastroesophageal (GE) Junction. The anchor can include a stent such as a wave anchor and is collapsible for catheter-based delivery and removal.