We present a freely downloadable program, InTune, designed to help musicians better hear and improve their intonation. The program uses the musical score from which the musician plays, assisting our approach in two ways. First, we use score following to automatically align the player’s audio signal to the musical score, thus allowing better and more flexible estimation of pitch. Second, we use the score match to present the tuning analysis in ways that are natural and intuitive for musicians. One representation presents the player with a marked-up musical score showing notes whose pitch characteristics deserve closer attention. Two other visual representations of audio overlay a musical time grid on the music data and allow random access to the audio, keyed by musical time. We present a user study involving 20 highly educated instrumentalists and vocalists.