Malnutrition in gastrointestinal disease can result from several pathogenetic mechanisms. The resulting clinical and laboratory features of malnutrition vary according to the specific pathogenetic factors involved. Many of the causes of malnutrition in gastroenterology are similar to those found in other acute and chronic diseases. However, certain disorders, specific to gastroenterology, may alter nutritional indices independent of the usual causes of malnutrition. These include small bowel bacterial overgrowth and protein-losing enteropathy. The impact of these disorders on the indexes of nutritional status is discussed.