Repetition is a basic indicator of musical structure. This study introduces new algorithms for identifying musical phrases based on repetition. Phrases combine to form sections yielding a two-level hierarchical structure. Automatically detected hierarchical repetition structures reveal significant interactions between structure and chord progressions, melody and rhythm. Different levels of hierarchy interact differently, providing evidence that structural hierarchy plays an important role in music beyond simple notions of repetition or similarity. Our work suggests new applications for music generation and music evaluation.