Fetal metabolic programming states that early life nutrition is implicated with the risk of later disease development and both under- and overnutrition during gestation might predispose individuals to develop obesity or diabetes later in life. Obesity operations called “gastric bypass” operations have shown unexpected involvement of the small intestine in diabetes pathophysiology as it in most cases result in a complete resolution of the diabetes before weight loss. Therefore we hypothesize that the small intestine is a subject of metabolic programming and that this programming can predispose for diabetes development. Twin-pregnant ewes where fed a Normal, a Low or a High diet during the last 6 weeks of gestation and the twin lambs where fed either a Conventional or a High fat, High carbohydrate (HCHF) diet during the first 6 months of life. Feeding challenge tests were performed on all lambs and some were slaughtered with collection of intestinal tissue for qPCR. The HCHF diet increased the blood level of glucose, insulin and TG and increased the intestinal expression of a range of genes involved in growth, vascularization as well as digestion and absorption. The maternal Low and High diet had effects on gene-expression, however the results vary between genes. These observations suggest that small intestine function has been programmed by the late-gestation Low or High diet at gene expression level, whereas the physiological metabolic functions has mainly been affected by the HCHF diet at such a young age. Further investigations on the long-term effects of early nutrition are required.