In his works he classified plants according to their fruits and seeds, rather than alphabetically or by medicinal properties. In 1555, he succeeded Luca Ghini as director of the botanic garden in Pisa. The botanist Pietro Castelli was one of his students. Cesalpino also did limited work in the field of physiology. He theorized a circulation of the blood. However, he envisioned a "chemical circulation" consisting of repeated evaporation and condensation of blood, rather than the concept of "physical circulation" popularized by the writings of William Harvey (1578–1657).
For his studies at the University of Pisa his instructor in medicine was R. Colombo (d. 1559), and in botany the celebrated Luca Ghini. After completing his course he taught philosophy, medicine, and botany for many years at the same university, besides making botanical explorations in various parts of Italy. At this time the first botanical gardens in Europe were laid out; the earliest at Padua, in 1546; the next at Pisa in 1547 by Ghini, who was its first director. Ghini was succeeded by Cesalpino, who had charge of the Pisan garden 1554-1558. When far advanced in years Cesalpino accepted a call to Rome as professor of medicine at University of Rome La Sapienza and physician to Pope Clement VIII. It is not positively certain whether he also become the chief superintendent of the Roman botanical garden which had been laid out about 1566 by one of his most celebrated pupils, Michele Mercati.
No comprehensive summing up of the results of Cesalpino's investigations, founded on a critical study of all his works has appeared, neither has there been a complete edition of his writings. Seven of these are positively known, and most of the seven have been printed several times, although none have appeared since the 17th century. In the following list the date of publication given is that of the first edition.
His most important philosophical work is Quaestionum peripateticarum libri V (1569). Cesalpino proves himself in this to be one of the most eminent and original students of Aristotle in the 16th century. His writings, however, show traces of the influence of Averroes, hence he is an Averroistic Aristotelean; apparently he was also inclined to pantheism, consequently he was included, later, in the Spinozists before Spinoza. A Protestant opponent of Aristotelean views, Nicolaus Taurellus wrote several times against Cesalpino. The work of Taurellus entitled Alpes caesae, etc. (1597), is entirely devoted to combating the opinions of Cesalpino, as the play on the name Caesalpinus shows. Nearly one hundred years later Cesalpino's views were again attacked by Samuel Parker, in a work entitled Disputationes de Deo et providentia divina (1678).
Cesalpino repeatedly asserted the steadfastness of his Catholic principles and his readiness to acknowledge the falsity of any philosophical opinions expounded by him as Aristotelean doctrine, which should be contrary to revelation. In Italy he was in high favour both with the secular and spiritual rulers.
Cesalpino is also famous in the history of botany as one of the first botanists to make an herbarium; one of the oldest herbaria still in existence is that which he arranged about 1550-60 for Bishop Alfonso Tornabono. After many changes of fortune the herbarium is now in the Museo di Storia Naturale di Firenze at Florence. It consists of 260 folio pages arranged in three volumes bound in red leather, and contains 768 species of plants. A work of some value for chemistry, mineralogy, and geology was issued by him under the title De metallicis libri tres (Rome, 1596). Some of its matter recalls the discoveries made at the end of the eighteenth century, as those of Antoine Lavoisier and René Just Haüy, it also shows a correct understanding of fossils.
The Franciscan monk Charles Plumier gave the name of Cesalpinia to a plant genus and Linnaeus retained it in his system. At the present day this genus includes approximately 150 species and belongs family Fabaceae, subfamily Caesalpinioideae, which contains a large number of useful plants. Linnaeus in his writings often quotes his great predecessor in the science of botany and praises Cesalpino in the following lines:
Quisquis hic exstiterit primos concedat honores
Casalpine Tibi primaque certa dabit.