Measurement in faeces of the principal nutrients, fat (F), water (W) and nitrogen (N) is useful to assess digestive and absorptive functions and thus to monitor patients' progress and response to therapy in malabsorption/maldigestion syndromes. Presently available techniques are not ideal in clinical practice for serial analyses as they are time-consuming and require unpleasant and prolonged handling of the stools. The present study aimed to evaluate the accuracy and precision of near infrared reflectance analysis (NIRA) in routine measurement of fat, nitrogen and water faecal contents compared with Van de Kamer (VDK), Kjeldahl (KJ) and gravimetric-by-lyophilization (LY) methods, respectively. Fat, nitrogen and water (n = 34), were measured in the 1-day faecal collections of 15 healthy subjects and 19 patients (10, coeliac disease; 6, chronic pancreatitis; 3, small-bowel Crohn's disease). A highly significant linear correlation was found between VDK, KJ, LY methods and NIRA analysis. Very low values of intra-assay coefficient of variation indicated a remarkable analytical precision of NIRA. A recovery test at different concentrations in the useful range was performed for all three nutrients, to assess the accuracy of NIRA. Quantitative recoveries were between 95 and 105%. Data from the present study show that NIRA analysis is reproducible, accurate and rapid (less than 1 min). These characteristics make NIRA serial analysis useful in clinical practice to monitor progress and response to therapy in patients with malabsorption/maldigestion syndromes.