Malabsorption encompasses dysfunctions occurring during the digestion and absorption of nutrients. A small proportion of patients presents with chronic diarrhoea. A clinical history supportive of malabsorption may guide investigations toward either the small bowel or pancreas. Serological testing for coeliac disease will determine most cases without invasive investigations. In the clinical context of persisting weight loss and malnutrition, small bowel enteropathy may be investigated with small intestinal biopsies. Small bowel absorptive capacity and permeability might be measured by oral sugar-mix ingestion. Further, approaches to the investigation of malabsorption might also involve the detection in faeces of a substance that has not been absorbed. A variation of the latter is the use of breath testing which relies on the breakdown of the malabsorbed test substance by colonic flora. Measurement of protein absorption is difficult and unreliable; it is, therefore, rarely advocated in clinical settings. No single biological marker confirming a diagnosis of small bowel malabsorption or small bowel integrity is presently available in clinical practice. Plasma citrulline concentration, an amino acid not incorporated into endogenous or exogenous proteins, has been extensively used in research studies and supportive results are establishing its concentration as a reliable quantitative biomarker of enterocyte absorptive capacity.