Methods of treatment using a gastrointestinal implant device removably anchored within an animal's gastrointestinal tract. For example, the implant device includes a collapsible anchor for anchoring the device coupled to a proximal end of a flexible sleeve. The implant device can be anchored within the stomach, within the pyloric orifice, and/or distal to the pylorus and extended into the duodenum. All partially-digested food, or chyme, exiting the stomach is funneled through the device. Methods of treatment include treating obesity by one or more of: limiting the absorption of nutrients within the duodenum; delaying the mixing of chyme with digestive enzymes; alter hormonal triggers; and providing negative feedback. Alternatively or in addition, the desired result includes treating a diseases, such as diabetes, or temporarily shielding a portion of the intestine to promote healing within the intestine.