Cystic fibrosis (CF) is the most commonly occurring lethal autosomal recessive disorder. The gene defect causes defective sodium and chloride transport across epithelial cells of the respiratory, hepatobiliary, gastrointestinal and reproductive tracts, resulting in thick mucus secretions. In the respiratory tract, mucus traps bacteria, causing repeated lung infections, progressive bronchiectasis and eventual death due to respiratory failure. In the gastrointestinal tract, mucus prevents pancreatic enzymes reaching the gut, leading to nutrient malabsorption. Careful nutritional management has a dramatic effect on growth and survival rates in CF. Appropriate nutritional support includes pancreatic enzyme replacement therapy, a high-fat/high-energy diet and essential nutrient supplementation, specifically fat-soluble vitamins and essential fatty acids (EFA). Long-term studies are required to examine the effects of nutritional interventions on key clinical outcomes in CF, such as the rate of decline of lung function. The use of circulating markers to assess the influence of nutritional therapy allows short-term intervention studies to predict the potential for clinical improvements. This article provides an overview of the biomarkers useful in the prediction of the efficacy of nutritional therapy on improvements in quality and quantity of life in CF.