Swammerdam was born in Amsterdam, the son of an apothecary and naturalist. He was destined for the Church; but he preferred the profession of medicine, taking his doctor's degree at Leiden in 1667. Having necessarily to interest himself in human anatomy, he devoted much attention to the preservation and better demonstration of the various structures, and he devised the method of studying the circulatory system by means of injections. He also spent much time in the study of insects, investigating the subject of their metamorphosis, and in this and other ways laying the beginnings of their natural classification, while his researches on the anatomy of mayflies and bees were also of great importance. His devotion to science led to his neglect of practice; his father, resenting this, stopped all supplies and thus Swammerdam experienced a period of considerable privation, which had the most unfortunate consequences to his health, both bodily and mental. In 1675 his father died, leaving him an adequate fortune, but the mischief was irreparable. He became a hypochondriac and mystic, joined the followers of Antoinette Bourignon, and died at Amsterdam.
His Algemeene Verhandeling van bloedeloose diertjens (1669) was published as The Natural History of Insects in English translation in 1792. This was the first important work on entomology, and described and classified hundreds of insects, arachnids and worms. His Biblia naturae, sive Historia insectorum in certas classes redacta was published after his death by Herman Boerhaave in 1737-1738. He was also the author of Miraculum naturae, sive Uteri muliebris fabrica .