Automatic analysis of digital audio with musical content is a difficult — but important — task for various applications in computer music, audio compression, and music information retrieval. This chapter contains a brief review of audio analysis as it relates to music, followed by three case studies of recently developed systems which analyse specific aspects of music. The first system is BeatRoot, a beat tracking system that finds the temporal location of musical beats in an audio recording, analogous to the way that people tap their feet in time to music. The second system is JTranscriber, an interactive automatic transcription system, which recognises musical notes and converts them into MIDI format allowing interactive monitoring and correction of the extracted MIDI data via a multimedia interface. The third system is the Performance Worm, a real time system for visualisation of musical expression, which presents in real time a two-dimensional animation of variations in tempo and loudness.