Watson entered the university in his native city of Chicago at the early age of 15, graduating in 1947. He obtained his PhD (1950) for studies of viruses at the University of Indiana and continued this work at the University of Copenhagen. In Copenhagen he realized that one of the major unsolved problems of biology lay in identifying the structure of the nucleic-acid molecules making up chromosomes. In 1951 he moved to the Cavendish Laboratory in Cambridge, England, to study the structure of DNA.

Early in 1953 Watson and Francis Crick published a molecular structure of DNA having two cross-linked helical chains (General Implications of the Structure of Deoxyribonucleic Acid). They arrived at this by considering possible geometric models, which they based on two independent sets of experimental work: the x-ray crystallography of Maurice Wilkins and Rosalind Franklin at King's College, London, and the earlier work of Ernst Chargaff, which had established the relative quantities of the organic bases present in the nucleic acids. Watson and Crick were able to show that certain organic bases linked the chains together by hydrogen bonds.

The model explains the three basic characteristics of heredity. It shows how genetic information can be expressed in the form of a chemical code; it demonstrates the way in which genes replicate themselves – when the two chains separate each can serve as a template for the synthesis of a new chain; and finally it provides an explanation of how mutations occur in genes, in terms of changes in the chemical structure of DNA. Watson, Crick, and Wilkins shared the Nobel Prize for physiology or medicine for this work in 1962.

Watson left Cambridge in 1953 for the California Institute of Technology. From 1955 to 1968 he worked at Harvard, becoming professor of biology in 1961. Here he continued to study the genetic code. In 1968 he became director of the Cold Spring Harbor Laboratory, New York, where he concentrated effort on cancer research. The same year he published The Double Helix, an informal, highly personal, and somewhat controversial account of the discovery of the structure of DNA. He retired in 1993.