The article provides the first description and analysis of the recently rediscovered manuscript titled Methodus anatomica by Girolamo Fabrici da Acquapendente (1533–1619). Acquapendente was one of the most important anatomists in late sixteenth-century Europe and played an instrumental role as Harvey’s teacher in Padua towards the latter’s discovery of the circulation of the blood. The manuscript provides first-hand testimony as to how anatomy was administered in Padua in the post-Vesalian era and sheds light on a number of otherwise unknown aspects of the development of the anatomical method. Chiefly among these is the attention devoted by Acquapendente to historia, as a way to order sensory data in a consistent way, which draws widely from the geometrical method and from the contemporary debate on the discretisation of continuous quantities.