While historians of the microscope currently consider that no programme of microscopy took place during the Enlightenment, the thesis challenges this view and aims at showing when and where microscopes were used as research tools. The focus of the inquiry is the research on microscopic animalcules and the relationship of European microscope making and practices of microscopy with topical trends of the industrial revolution, such as quantification. Three waves of research are characterised for the research on animalcules in the Enlightenment: 1. seventeenth-century observations on animalcules crowned by Louis Joblot's 1718 works in the milieu of Paris Académie royale des sciences, 2. mid eighteenth-century observations and experiments on polyps and animalcules (Trembley, Baker and Hill) and, 3. between 1760 and 1790, OF Müller's establishment of the systematics of infusoria in Denmark and Germany.