Aldrovandi was born in Bologna to a noble family, which sent him to apprentice with merchants, but he found his vocation, after studying humanities and law at the universities of Bologna and Padua and becoming a notary. Successively his interests went out to philosophy and logic which he combined with the study of medicine.

He obtained a degree in medicine and philosophy in 1553 and started teaching logic and philosophy in 1554 at the University of Bologna. In 1559 he became professor of philosophy and in 1561 he became the first professor of natural sciences at Bologna (lectura philosophiae naturalis ordinaria de fossilibus, plantis et animalibus).