Transcriptomic analysis was first applied on different intestinal sections of Atlantic salmon fry. The fish were fed either vegetable oil or fish oil from first-feeding. Samples were taken at day 0 (0.16g), 65 (2.5g) and 100 (10g). The intestines were dissected into three sections, stomach, pyloric caeca and hindgut, and applied separated for RNA-seq. Gene expressions were compared between different tissues, developmental stages and dietary treatments.