The microscope was one of the most important inventions of the scientific revolution. Giovanni Faber, a member of the Accademia dei Lincei, gave the instrument its name in 1625. The first microscopes were compound models, formed by a system of lenses inserted in a rigid tube. A better optical performance was achieved by the simple microscope, consisting of a single lens. The simple microscope became popular in the second half of the seventeenth century. Naturalists preferred it, chiefly for fieldwork and dissection. The performance of the first compound microscopes was severely limited by aberration. The problem was solved in the first half of the nineteenth century, partly thanks to Giovan Battista Amici. The items displayed enable us to follow the gradual progress from the first compound microscopes, of the Galilean type, to the extremely complex instruments crafted by the great English and German makers and fitted with sophisticated accessories. Of the large group of Italian instruments in the collection, the microscopes produced by Giovan Battista Amici and by Filippo Pacini in the nineteenth century deserve special mention for their technical quality and for their innovative research applications.