Gastric inhibitory polypeptide (GIP, glucose-dependent insulinotropic polypeptide) is expressed by intestinal K cells to regulate glucose-induced insulin secretion. The impact of Roux-en Y bypass (RYGB) surgery on blood GIP is highly contraversial. This study was conducted to address the mechanism of controversy. GIP mRNA was examined in the intestine, and serum GIP was determined using Luminex and ELISA in diet-induced obese (DIO) mice. The assays were conducted in RYGB mice in fasting and fed conditions. Food preference, weight loss and insulin sensitivity were monitored in RYGB mice. In DIO mice, GIP mRNA was increased by 80% in all sections of the small intestine over the lean control. The increase was observed in both fasting and fed conditions. After RYGB surgery, the food-induced GIP expression was selectively reduced in the Roux-limb, but not in the biliopancreatic and common limbs of intestine in fed condition. Lack of stimulation by glucose or cholesterol contributed to the reduction. Jejunal mucosa of Roux-limb exhibited hypertrophy, but villous surface was decreased by the undigested food. Serum GIP (total) was significantly higher in the fasting condition, but not in the fed condition due to attenuated GIP response to food intake in RYGB mice. The GIP alteration was associated with chow diet preference, sustained weight loss and insulin sensitization in RYGB mice. RYGB increased serum GIP in the fasting, but not in the fed conditions. The loss of food-induced GIP response in Roux-limb of intestine likely contributes to the attenuated serum GIP response to feeding.