This report describes a case of refractory enteropathy with circulating intestinal goblet cell autoantibodies (IGA). A 19 year old man with hyperthyroidism had suffered from protracted diarrhoea for nearly 10 years. Histological examination showed evidence of collagenous enterocolitis. The diarrhoea did not improve despite fasting under total parenteral nutrition. An immunofluorescence assay demonstrated IGA without anti-enterocyte autoantibodies, the hallmark of autoimmune enteropathy, although other criteria were fulfilled. None of 109 controls, including 55 cases of inflammatory bowel disease and one of lymphocytic colitis, had IGA. This case is considered to be a variant of autoimmune enteropathy, and might be a distinct entity.