Common marmosets (Callithrix jacchus) are frequently used for biomedical research but gastrointestinal diseases have been major health problems to maintain captive marmosets. We have diagnosed a novel gastrointestinal disease in marmosets, as which we propose to call 'marmoset duodenal dilation syndrome'; this disease is characterised by proximal duodenal obstruction and dilation. This study aimed to reveal the clinical and pathological findings of this syndrome and establish appropriate diagnostic imaging methods. Animals with the syndrome comprised 21.9% of the necropsy cases at the Central Institute for Experimental Animals in Kawasaki, Japan. The syndrome is characterised by clinical signs included vomiting, bloating, and weight loss. Grossly, all diseased animals exhibited significant dilation of the descending part of the duodenum, which contained a mixture of gas and fluid. The duodenal dilations were definitively diagnosed by contrast radiography. Moreover, a combination of plain radiography and ultrasonography was found to be a viable screening method for diagnosing duodenal dilation. The animals with duodenal dilation characteristically showed adhesions between the descending duodenum and ascending colon with chronic peritonitis. The cause of marmoset duodenal dilation syndrome remains unknown, but was likely multifactorial, including peritoneal adhesion, chronic ulcer, and feeding conditions in this study.