Many years later, in 1740, Morgagni edited a collected edition of Valsalva's writings, with important additions to the treatise on the ear, and with a memoir of the author. When Valsalva was transferred to Parma, Morgagni succeeded to his anatomical demonstratorship. At this period he enjoyed a high repute in Bologna; he was made president of the Academia Enquietorum when in his twenty-fourth year, and he is said to have signalized his tenure of the presidential chair by discouraging abstract speculations, and by setting the fashion towards exact anatomical observation and reasoning.

He published the substance of his communications to the Academy in 1706 under the title of Adversaria anatomica, the first of a series by which he became favorably known throughout Europe as an accurate anatomist; the book included Observations of the Larynx, the Lachrymal Apparatus, and the Pelvic Organs in the Female. After a time he gave up his post at Bologna, and occupied himself for the next two or three years at Padua, where he had a friend in Domenico Guglielmini (1655-1710), professor of medicine, but better-known as a writer on physics and mathematics, whose works he afterwards edited (1719) with a  biography. Guglielmini desired to see him settled as a teacher at Padua, and the unexpected death of Guglielmini himself made the project feasible, Antonio Vallisneri (1661-1730) being transferred to the vacant chair, and Morgagni succeeding to the chair of theoretical medicine. He came to Padua in the spring of 1712, being then in his thirty-first year, and he taught medicine there with great success until his death on the 6th of December 1771.

While in his third year in Padua an opportunity occurred for his promotion (by the Venetian senate) to the chair of anatomy, in which he became the successor of an illustrious line of scholars, including Vesalius, Gabriele Falloppio, Geronimo Fabrizio, Gasserius, and Adrianus Spigelius, and in which he enjoyed a stipend that was increased from time to time by vote of the senate until it reached twelve hundred gold ducats. Shortly after coming to Padua he married a lady of Forlì, of noble parentage, who bore him three sons and twelve daughters. Morgagni enjoyed an unparalleled popularity among all classes. He was of tall and dignified complexion, with blonde hair and lilac eyes, and with a frank and happy expression; his manners were polished, and he was noted for the elegance of his Latin style. He lived in harmony with his colleagues, who are said not even to have envied him his unprecedentedly large stipend; his house and lecture-theatre were frequented tanquam officina sapientiae by students of all ages, attracted from all parts of Europe; he enjoyed the friendship and favor of distinguished Venetian senators and of cardinals; and successive popes conferred honours upon him.

Not long after moving to Padua the students of the German nation, of all the faculties there, elected him their patron, and he advised and assisted them in the purchase of a house to be a German library and club, for all time. He was elected into the imperial Caesareo-Leopoldina Academy in 1708 (originally located at Schweinfurth), and to a higher grade in 1732, into the Royal Society in 1724, into the Paris Academy of Sciences in 1731, the St. Petersburg Academy in 1735, and the Berlin Academy in 1754. Among his more celebrated pupils were Antonio Scarpa (who died in 1832, connecting the school of Morgagni with the modern era), Domenico Cotugno (1736-1822), and Caldani (1725-1813), the author of the magnificent atlas of anatomical plates published in 2 volumes at Venice in 1801-1814.

In 1761, when he was in his eightieth year, he wrote the great work which made pathological anatomy a science, and diverted the course of medicine into new channels of exactness or precision—the De Sedibus et causis morborum per anatomem indagatis, which during the succeeding ten years was reprinted several times (thrice in four years) in its original Latin, and was translated into French (1765), English (1769), and German (1771).  The only special treatise on pathological anatomy previous to that of Morgagni was the work of Théophile Bonet of Neuchâtel, Sepulchretum: sive anatomia practica ex cadaveribus morbo denalis, first published 1679, three years before Morgagni was born; it was republished at Geneva in 1700, and again at Leiden in 1709. Although the normal anatomy of the body had been comprehensively, and in some parts exhaustively, written by Vesalius and Fallopius, it had not occurred to any one to examine and describe systematically the anatomy of diseased organs and parts. Morgagni has narrated the circumstances under which the De Sedibus took origin. Having finished his edition of Valsalva in 1740, he was taking a holiday in the country, spending much of his time in the company of a young friend who was curious in many branches of knowledge. The conversation turned upon the Sepulchretum of Bonet, and it was suggested to Morgagni by his dilettante friend that he should put on record his own observations. It was agreed that letters on the anatomy of diseased organs and parts should be written for the perusal of this favoured youth (whose name is not mentioned); and they were continued from time to time until they numbered seventy. Those seventy letters constitute the De sedibus et causis morborum, which was given to the world as a systematic treatise in 2 vols., folio (Venice, 1761), twenty years after the task of epistolary instruction was begun.