Malnutrition is associated with many chronic diseases, though its extent and effect is not well known. Measurement of body protein provides a quantitative and reproducible means of monitoring malnutrition. Results for anorexia nervosa, end stage renal failure value and asymptomatic and symptomatic HIV positive subjects are presented to show that, with the exception of asymptomatic HIV subjects, substantial protein depletion does occur. A more difficult problem is to determine the relation between body protein, the effects of treatment and prognosis. In the case of CAPD patients, 20% protein depletion was found to be associated with a poor prognosis. For anorexia nervosa subjects, readmission probability was found to be correlated with body protein. However, monitored refeeding and exercise achieved a more normal body composition and quality of life. The critical effect of protein depletion in AIDS remains to be determined, but once ascertained, the role of enteral and parenteral supplementation can then be quantitatively examined.