The foundations of microscopic anatomy were laid in the 17th C., first by Federico Cesi and Francesco Stelluti in Apiarium, then by Giovanni Battista Hodierna in Occhio della mosca and Marco Aurelio Severino in Zootomia Democritaea. But its full potential was developed by Marcello Malpighi. Just as Galileo had initiated with the telescope the exploration of the great machine of the universe, so Malpighi set out with the microscope to reveal the hidden structure of the machine of the human body.

In the 17th C., thanks to René Descartes and Giovanni Alfonso Borelli, the new method of mechanistic physiology progressively replaced old Galenic medicine. The causes of organic functions were henceforth sought in the minute structure of organs—in the secret mechanisms of the fibers, fluids, and particles revealed by the microscope. In 1665, Robert Hooke was the first to observe plant cells, although his discovery had no practical consequence. This concept of the workings of life reached its apogee with Giovanni Battista Morgagni, who laid the foundations of modern pathological anatomy.

Thanks to the combination of "subtle" anatomy and of microscopic magnification, all of human and animal anatomy was rewritten in a short period of time: Thomas Bartholin discovered the lymph vessels; Malpighi observed the alveolar structure of the lungs, the papillar receptors of the tongue and the direct connection between arteries and veins; he also identified red blood cells and gave a precise description of the first phases of the embryonic development of the chick; Lorenzo Bellini revealed the structure and function of kidneys; Francesco Redi illustrated the extraordinary complexity of the organization of insects; Thomas Wharton formulated the theory of glands as secretory organs; Niels Stensen and Giovanni Alfonso Borelli described the dynamics of muscular movement; Thomas Willis and, later, Albrecht von Haller investigated the structure of the nervous system and the dynamics of neuro-muscular functions.