Maclyn McCarty was born in South Bend, Indiana. His father worked for the Studebaker Corporation in South Bend and was sent to various locations around the country. His family moved with him and McCarty's early education was itinerant until they settled back in South Bend in 1922. His parents were both extremely well-read and they encouraged their children to be self-sufficient in the pursuit of knowledge.

In high school, McCarty read a book called Microbe Hunters. This led to other books on biology and medicine and helped McCarty decide on a career in medical research. As a prelude to later research, McCarty and three of his high school friends formed the "Amateur Research Chemists" Club and did experiments in their basement labs.

In 1929, McCarty went to Stanford University for premed training and in 1933 started medical school at Johns Hopkins University. He spent a few summers as a pediatrics intern but by the time he graduated medical school, McCarty was working in a clinical research lab.

After graduation, McCarty looked for a research position, a scarcity because of the war. In 1940, he accepted a position for $100 a month to work with William Tillet at New York University. The next year, McCarty obtained a fellowship from the National Research Council. Their recommendation was that McCarty use the fellowship in another lab to broaden his experimental horizons. Tillet made arrangements for McCarty to join Oswald Avery's lab at the Rockefeller Research Institute. Tillet had worked in Avery's lab in the 20's and thought that it was the natural place for McCarty to go to pursue his interest in bacteriological research.

At the Rockefeller, McCarty worked with Avery to perfect the purification of the Pneumococcus transforming factor, and they were the first to precipitate DNA from bacteria. They used enzymes to degrade different classes of molecules and proved that DNA was the transforming factor. Their landmark paper was published in 1944. McCarty had been drafted in 1942 and did most of the work in a naval uniform as part of the naval research unit based at Rockefeller Hospital.

In 1946, McCarty was given his own research lab at the Rockefeller Institute. He was professor emeritus of the Rockefeller University, which evolved from the Rockefeller Research Institute.