We report the RNAseq data from captive common marmosets with gastrointestinal diseases housed at MIT. Samples were collected at necropsy from the duodenum and jejunum from 3 animals presenting with intestinal bowel disease (IBD) and 3 animals with duodenal strictures/ulcers. To determine the transcriptomic profile of animals with strictures, we evaluated the duodenal tissue immediately adjacent to the stricture lesion and compared it to the duodenum of non-stricture (IBD) animals as a non-stricture control. To determine the transcriptomic profile of animals with IBD, we evaluated the jejunum of animals with IBD with the jejunum of non-IBD (stricture) animals as a non-IBD control. Minimal pathology was observed in the non-IBD control but enteritis was noted in non-stricture controls. We report that stricture may affect the intestinal absorption and lipid metabolism in marmosets, while IBD increases immune responses. Overall design: Examination of ulcers/stricture in the duodenum and IBD in the jejunum of marmosets.