Flutists encounter significant physical problems in the course of their everyday playing of the instrument and frequently are not given the detailed and accurate scientific teaching and training that would prevent the problems in the first place. The purpose of this study is to investigate the prevalence and scope of performance-related problems among flutists and then to provide science-based teaching about how the body organizes itself to play the flute. Physical difficulties related to playing the flute are analyzed through a large-sample online survey and personal interviews with six prominent flutists. The second half of the document is a scholarly application of the scientific knowledge of anatomy, physiology, and neurology to the physical action of flute playing. The survey data encompasses the combined responses of 181 respondents with results indicating that a majority of flutists experience pain related to their playing yet have little training in prevention. The dramatic stories of performance-related injuries by the selected interviewees serve to underscore the need for more education for musicians and research by scientists in the field of performance arts medicine. Applying the facts and principles of anatomy, physiology, and neurology to the playing of the flute presents today's flutists with many new science-based concepts to consider while they are practicing or performing. Because of the asymmetrical body position required to play the flute and the unstopped arrangement of our embouchure, flutists must put more emphasis on achieving a healthy posture and balanced stance for playing that supports the active respiratory demands of the instrument.