Running is a basic form of human locomotion and one of the most popular sports worldwide. While the leg biomechanics of running have been studied extensively, few studies have focused on upper-body movement. However, an effective arm swing and longitudinal rotation of the shoulders play an important role in running efficiency as they must compensate for the longitudinal torques generated by the legs. The aim of this study is to assess the upper-body rotation using wearable inertial sensors and to elucidate its relation to energy expenditure. Eighty-six junior elite middle- and long-distance runners (37 female, 49 male) performed an incremental treadmill test with sensors attached on both shoulders, tibiae and the sacrum. The mean and total horizontal shoulder and pelvis rotations per stride were derived while energy costs were determined using respiratory gas analysis and blood sampling. Results show that shoulder and pelvis rotations increase with running speed. While shoulder rotation is more pronounced in female than in male runners, there is no sex difference for pelvis rotation. The energy cost of running and upper trunk rotation prove to be slightly negatively correlated. In conclusion, upper body rotation appears to be an individual characteristic influenced by a sex-specific body mass distribution.