The efficacy of stereotactic body radiotherapy (SBRT) has been well demonstrated. However, it presents unique challenges for accurate planning and delivery especially in the lungs and upper abdomen where respiratory motion can be significantly confounding accurate targeting and avoidance of normal tissues. In this paper, we review the current literature on SBRT for lung and upper abdominal tumors with particular emphasis on addressing respiratory motion and its affects. We provide recommendations on strategies to manage motion for different, patient-specific situations. Some of the recommendations will potentially be adopted to guide clinical trial protocols.