Cystic fibrosis (CF) is characterized by deteriorating lung function and mal-digestion, which result in growth failure and/or under-nutrition. Several factors, alone or combined, contribute to malnutrition in CF: poor energy intake, elevation of energy loss as a result of malabsorption, increasing resting energy expenditure due to genetic mutation and/or pulmonary exacerbation. Several techniques have been used to assess energy expenditure and physical activity in order to better understand mechanisms of malnutrition in CF and follow therapeutic interventions. Indirect calorimetry (IC) studies have shown that resting energy expenditure (REE) was 10-22% higher than predictive values. This increase could be attributed to chronic inflammation as a result of Pseudomonas aeruginosa (PA) infection. Indeed, intravenous antibiotic therapy decreases REE. Doubly labelled water technique and heart rate monitoring calibrated against IC techniques shows that total energy expenditure (TEE) was not different than in healthy children. Physical activity level assessed by the ratio TEE-REE is also not different between CF of healthy children. Recently, new accelerometry technics, easier to use and less invasive have been successfully used in order to assess physical activity level in CF. Precise and ambulatory assessment of energy expenditure and physical activity permit to check and adapt dietary allowances in CF. These techniques could be simultaneously used and be helpful to assess efficacy of intervention studies.