Musical set theory uses the language of mathematical set theory in an elementary way to organize musical objects and describe their relationships. To analyze the structure of a piece of (typically atonal) music using musical set theory, one usually starts with a set of tones, which could form motives or chords. By applying simple operations such as transposition and inversion, one can discover deep structures in the music. Operations such as transposition and inversion are called isometries because they preserve the intervals between tones in a set.

Expanding on the methods of musical set theory, some theorists have used abstract algebra to analyze music. For example, the pitch classes in an equally tempered octave form an abelian group with 12 elements. It is possible to describe just intonation in terms of a free abelian group.[16][17]

Transformational theory is a branch of music theory developed by David Lewin. The theory allows for great generality because it emphasizes transformations between musical objects, rather than the musical objects themselves.

Theorists have also proposed musical applications of more sophisticated algebraic concepts. The theory of regular temperaments has been extensively developed with a wide range of sophisticated mathematics, for example by associating each regular temperament with a rational point on a Grassmannian.