Cow's milk protein enteropathy is a symptom complex that composed of severe diarrhoea and malnutrition. This disorder is caused by non-immunoglobulin E-mediated food allergy. Its clinical features and natural course have been explained in many reports, of different types of cow's milk and soy reactions. In the present article, we describe a newborn patient who presented with chronic diarrhoea and failure to thrive diagnosed as cow's milk protein enteropathy. The duodenal biopsy revealed granulomatous duodenitis which has not been described before. Her clinical and pathological findings responded well to cow's milk elimination. We suggest that food allergies should be considered in differential diagnosis of patients with chronic diarrhoea and failure to thrive.