Autoimmune enteropathy is a rare intestinal disease. Here we report an elderly female with autoimmune enteropathy and primary biliary cholangitis who presented with chronic diarrhea, malnutrition and severe hypokalemia and metabolic acidosis. Enteroscopy showed atrophied small intestinal villi with scallop-like and fissure-like changes. Hormone treatment relieved diarrhea. Four months later, she developed primary biliary cholangitis, and the liver function returned to normal after treatment with ursodeoxycholic acid, corticosteroids and immunosuppressants.