In 1551, he was invited to occupy the chair of anatomy and surgery at the University of Padua and also lectured on medicinal plants or botany.

His description of the lacrimal ducts in the eye was a marked advance on those of his predecessors and he also gave a detailed account of the ethmoid bone and its cells in the nose.

He studied the reproductive organs in both sexes, and gave the first precise description of the uterine tube, which leads from the ovary to the uterus and bears his name to this day.

He was the first to describe the ileocecal valve, which prevents a reflux of fecal matter from the colon to the small intestines, and demonstrated its function to his students.

After his death, some of his students published their lectures, in particular, on ulcers, tumors, medical cosmetics, and other surgical topics and on botany and mineral waters.

In his lectures, Falloppio also described, around 1555, a linen sheath that previously had been soaked in medicinal substances and then dried and some authors have praised him as the inventor of condom.

He argued against Fracastor's theory of fossils, as described as follows in Charles Lyell's Principles of Geology: Falloppio of Padua conceived that petrified shells had been generated by fermentation in the spots where they were found, or that they had in some cases acquired their form from 'the tumultuous movements of terrestrial exhalations.'

Although a celebrated professor of anatomy, he taught that certain tusks of elephants dug up in his time at Puglia were mere earthy concretions, and, consistently with these principles, he even went so far as to consider it not improbable, that the vases of Monte Testaceo at Rome were natural impressions stamped in the soil.