The aim of this study was to examine the presence or absence of dietary transgenic (Roundup Ready® soybean – RRS®) and soybean DNA (sRubisco) in the intestinal tract of Atlantic salmon fed either genetically modified (GM) or conventional (non-GM) soybeans. Uptake of dietary DNA was evaluated in the post gastric intestine (pyloric ceca – PC, mid intestine – MI and distal intestine – DI) after continuous feeding (6 months), feed restriction and re-feeding using qPCR and in situ hybridization. No transgenic DNA fragments were detected in any of the intestinal samples using event specific primers. Soybean DNA was detected in all segments of the intestinal tissue (PC, MI and DI) and visualized in the cell vacuolar system of the DI in the apex area of the intestinal fold. Dietary DNA was gradually cleared from the intestinal tissues when feed was restricted and could not be detected after 5 days. Re-feeding resulted in dietary plant DNA uptake after 2 h. The results show that the salmon intestine is able to take up dietary plant DNA shortly after feed intake and that one of the factors affecting uptake and clearance of nucleic acids in the various intestinal segments are the feeding status of the fish.