We describe a method of automatically creating a content-based index of musical scores. The goal is to capture the themes, or motifs, that appear in the music. The method was tested by building an index of 25 orchestral movements from the classical music literature. For every movement, the system captured the primary theme, or a variation of the primary theme. In addition, it captured 13 of 28 secondary themes. The resulting index was 14% of the size of the database. A further reduction of 2% is possible; however, this discards secondary themes. A listening experiment using five orchestral movements showed that people can reliably recognize secondary themes after listening to a piece of music-therefore, it may be necessary to retain secondary themes in a score index.