Swammerdam, an Amsterdam apothecary's son, studied medicine at Leiden University, graduating in 1667. However he never practiced and instead devoted his life to microscopical studies of a widely varying nature. His most important work, namely the discovery and description of red blood corpuscles in 1658, was completed before he went to university. He later demonstrated experimentally that muscular contraction involves a change in the shape but not volume of the muscle. He also studied movements of the heart and lungs and discovered the valves in the lymph vessels that are named for him.

Swammerdam is also remembered for his pioneering work on insects. He collected some 3000 different species and illustrated and described the anatomy, reproductive processes, and life histories of many of these. This work, together with his system of insect classification, laid the foundations of modern entomology. Swammerdam's Biblia naturae (Book of Nature), published long after his death (1737–38), still stands as one of the finest one-man collections of microscopical observations.

At the theoretical level Swammerdam developed a new argument in support of the preformationist position, the view that organisms are born already formed. His argument, first presented in his Historia insectorum (1669; Account of Insects), was based upon the nature of insect metamorphosis. At first sight it might appear that the metamorphic process supported the alternative view of development, epigenesis, the claim that organisms develop gradually and in sequence. Swammerdam, however, revealed a different picture when, with the aid of a microscope, he succeeded in identifying structures belonging to butterflies in pupae and caterpillars. The caterpillar, Swammerdam insisted, was not changed into a butterfly, rather grew by the expansion of parts already formed. Nor does the tadpole change into a frog; it becomes a frog “by the infolding and increasing of some of its parts.” In proof of his position Swammerdam would display a silkworm to his critics, peel off the outer skin, and display the rudiments of the wings within.

In the same work Swammerdam added one more piece of evidence against the claim that organisms can generate spontaneously. Insects found in plant galls, he pointed out, developed from eggs laid therein by visiting flies.