He spent most of his life at the University of Padua, where he studied under the eminent anatomist Gabriel Fallopius. As Fallopius' successor to the chair of surgery and anatomy (1562–1613), Fabricius built a reputation that attracted students from all of Europe. The English anatomist William Harvey (Harvey, William) was his pupil. In De Venarum Ostiolis (1603; “On the Valves of the Veins”), Fabricius gave the first clear description of the semilunar valves of the veins, which later provided Harvey with a crucial point in his famous argument for circulation of the blood.

Fabricius' De Formato Foetu (1600; “On the Formation of the Fetus”), summarizing his investigations of the fetal development of many animals, including man, contained the first detailed description of the placenta and opened the field of comparative embryology. He also gave the first full account of the larynx as a vocal organ and was first to demonstrate that the pupil of the eye changes its size.