The culmination of the doctoral program is the comprehensive exam. This is a two-part exam taken in the second year of study or anytime thereafter. Part I of this exam is the written section. This consists of three hours of history and four hours of theory tests of a broad, general nature. It is important to understand that these tests are not a measure of what the student learned in the two years of course work taken at Manhattan School of Music, but are rather an evaluation of his or her total experience with the history, literature, and theory of music gained over many years of working as a musician.

The written history exam covers all periods from early Christian music to the present. Students are expected to demonstrate a familiarity with major composers, forms, genres, styles, literature, etc. The theory exam is similar. Knowledge of basic skills in harmony and counterpoint as well as the ability to think analytically are tested.

Part II of the exam is the oral portion, which takes place a month after the written exam. Students are only allowed to take this exam if they pass the written exam. In the oral exam students appear before a small committee of faculty to answer questions related to the history of their instrument, its major repertoire, and a theoretical understanding of that repertoire.

Both portions of the comprehensive exam must be passed before proceeding to the writing of the thesis.