Fabricius was born at Aquapendente in Italy and educated at the University of Padua where he studied under Gabriel Fallopius, succeeding him, in 1565, as professor of anatomy.

As an anatomist his most significant work was his De venarum ostiolis (1603; On the Valves of the Veins), which contains a clear and detailed description of the venous system and which exercised a considerable influence on his most famous pupil, William Harvey. Fabricius himself entertained no such idea as the circulation of the blood, explaining the role of the valves as retarding the blood flow, thus allowing the tissues to absorb necessary nutriment.

He spent much time observing the development of the chick embryo and published two works De formato foetu (1600; On the Formation of the Fetus) and De formatione ovi et pulli (1612; On the Development of the Egg and the Chick). These were hailed as elevating embryology into an independent science but they still contain many incorrect assumptions.

Thus for Fabricius semen did not enter the egg but rather initiated the process of generation from a distance in some mysterious way. He also made a now totally unfamiliar distinction between what nourishes and what produces the embryo. Thus he believed both the yolk and albumen merely nourished the embryo. Having eliminated the sperm, yolk, and albumen, Fabricius claimed that the chalaza – the spiral threads holding the yolk in position – produces the chick.

It was while engaged upon this work that he discovered and described the bursa of Fabricius. This is a small pouch in the oviduct of the hen, which Fabricius thought to be a store for semen. In the 1950s however the young research student B. Glick showed that this obscure organ plays a key role in the immune system of chickens, and by implication of humans who must possess a comparable system.