The time dependent character of data generated by modern calorimetry equipment provides the unique opportunity to monitor short term changes in energy expenditure related to physical activity, feeding pattern and other experimental interventions. When timed recordings of physical activity are available, total heat production can be decomposed into heat production due to physical activity and resting metabolism. Based on additional measurements and assumptions, further separation of the thermic effect of feeding is possible. When separating total heat production into its components, the separation of activity energy is a key step, even if activity energy is not the main interest of the study. This chapter provides an overview of a current methodology used to measure physical activity within the setting of indirect calorimetry. An approach to decompose total heat production into activity related and resting metabolic rate, the latter including the short term effect of feeding, is presented. In regression analysis, the energetic costs of each unit of physical activity, as well as the resting metabolic rate are assumed to be constant. Improved methodology is available using penalized least squares regression to model time dependent variation in the resting metabolic rate. The impact of experimental variables and settings, e.g. sampling frequency and chamber washout time are discussed. In addition, housing conditions, including ambient temperature, and feeding methods can impact on the relationship between physical activity and total heat production, affecting the reliability with which total heat production can be decomposed into resting metabolic rate and heat production related to physical activity. Finally, single housing conditions, often difficult to avoid in indirect calorimetry experiments, can modify behaviour, induce stress and therefore substantially influence activity related heat production and the results of calorimetry experiments. The effect of single vs group housing in growing pigs extracted from previously unpublished data and from the literature, suggest that single housing may increase activity heat production possibly because of induced stress. From behavioural and calorimetry data obtained in calves it is also demonstrated that the energetic costs of stereotyped behaviours can be very high.