Disease-related malnutrition is frequent in patients with chronic pulmonary diseases. Though there is no doubt about the usefulness of Oral Nutritional Supplements (ONS) in managing malnutrition in such patients, only a handful of publications are available in the literature on clinical trials with ONS in this patient population. Since the digestion of macronutrients results in a strain on the respiratory functions in severe pulmonary diseases, the source of energy may also play a crucial role in the efficacy of nutrition with ONS in such patients. Here we present the study protocol of a randomized, open-label, multicentre clinical trial aimed to determine whether a new, condition-specific ONS (with a composition tailored to the needs of patients with decreased pulmonary functions) is more effective compared to a general ONS in improving the nutritional status in patients with compromised respiratory functions.