He served as an assistant to Marcello Malpighi, beginning in Bologna in 1691 and following him to Rome the next year when Malpighi was named chief personal physician ("archiater") to the pope. While serving under Malpighi, Baglivi performed experiments on the circulation of blood in frogs; he also injected various medicines into dogs' veins and spinal canals and experimented on their pneumogastric nerves. He utilized a microscope to study the structure of muscles and the brain. Following Malpighi's death in 1694, Baglivi performed his autopsy and gave an thorough description of the cerebral apoplexy that killed him. While in Rome, he befriended Bellini, Lancisi, Redi, Tozzi, and Trionfetti. In 1695, he became second physician to Pope and, in 1696, was elected professor of anatomy at the College of Sapienza. He received memberships in Rome's Academy of the Arcadians (1699) and the Tuscan "Fisiocriti" (1700). He continued as a personal physician to and was named the Sapienza's professor of theoretical medicine in 1701. He continued his observations by microscope as professor of theoretical medicine at the Sapienza, as well as examining the properties of saliva, bile, and blood. His lectures, demonstrations, and consultations became famed across Europe: he was elected a Fellow of the Royal Society in England in July 1698, a member of the Holy Roman Empire's Academy of the Curious in 1699, and an "honorary member" ("") of the French Academy. For a time he was surrounded in controversy following charges of plagiarism by Antonio Pacchioni, but Baglivi successfully defended the primacy of his own work.