Martin Arrowsmith, the novel's protagonist, is born and raised in the small Midwestern town of Elk Mills where he develops an interest in science and spends his free hours reading through Gray's Anatomy and other books in the office of the town's doctor, Doc Vickerson. This early education is supplemented when he goes off to college and eventually becomes a medical student at the University of Winnemac, where he meets his life-time mentor, Max Gottlieb, a German professor committed to laboratory science and research.

While in medical school, Martin dates a girl named Madeleine Fox, a snobbish, educated doctoral student of literature and becomes engaged to her, only to leave her later for Leora Tozer, a down-to-earth nurse in training, whom he will love and live with until the end of her life. Also, while at Winnemac, under the wing of Gottlieb, Martin develops a deep-rooted love for the laboratory and lashes out against "commercialism" and the faults of the practicing physician versus the ideals of true science and research. Nevertheless, Martin, after graduating from Winnemac, must abandon his "true science" because he has married Leora and now has a wife to support.

Martin and Leora move to Leora's hometown of Wheatsylvania where Martin becomes a country doctor about whom the townspeople gossip. Although he is at times successful, he never gains the trust of the community as a whole and loses a patient, in his early days. Leora also has a miscarriage during their time in Wheatsylvania. Feeling as though he has failed in Wheatsylvania, Martina and Leora move to Nautilus, a city in the Midwest.

In Nautilus, Martin becomes a public health physician, working under Dr. Pickerbaugh, who is more of a salesman than a doctor and who writes verses about hygiene and cleanliness. After being unhappy in Nautilus, Martin is called to the Rouncefield Clinic in Chicago to work with his medical school colleague, with whom he had always been in competition, Angus Duer. His work as a pathologist in the Rouncefield Clinic, however, also proves disheartening given that the Clinic is a playground for doctors who care more for money than anything else.

It is at this point that Martin comes to the attention of Max Gottlieb once again. Gottlieb, who is working at the prestigious McGurk Research Institute in New York (modeled after the Rockefeller Institute in New York), invites Martin to join the research team. He is glad to finally have his chance at laboratory science, the "true science" he had had to abandon. Martin is happy there until he begins to be rushed in his study and work. The heads of the Institute begin to pry into his research in order to apply pressure on Martin to publish and "sell" his work. While at the institute, however, Martin comes across a huge triumph in his research, the isolation of a bacteriophage that seems to kill pneumonia and plague.

Although there is some initial disappointment at finding out that much of his research had already been done and published by another scientist, Martin decides to further his research and is successful in his continuations. Martin is later sent to test his discovery in the Caribbean island of St. Hubert, which is infested with plague. Martin agrees to conduct his experimental research on the quarantined island of St. Hubert. Leora accompanies him.

On the island of St. Hubert, Martin is meant to conduct further research on the phage in order to understand it better, and he does, in fact, seem to cure the people of the plague. However, the research conducted on the island is not altogether precise because Martin had given up on his work for a time, after the tragedy of his wife's (Leora) death due to the plague. Martin goes through a period of mourning in which he abandons his research, a period which he will later be upset by and consider a failure on his behalf.

It is also on the island that Martin meets Joyce Lanyon, an immensely wealthy woman whom he marries when he returns to New York, after Leora's death. Martin, however, cannot grow fully accustomed to his new wife's rich ways and finds himself, once again, unhappy. He, therefore, abandons her and his child with her in order to retreat into the woods with Terry Wickett, his friend and colleague from the McGurk Institute. The book ends with Martin and Terry's plan to build a laboratory in Terry's home in the woods so that they may be left to do the important research they so love and need without the commercial pressure imposed by department heads and the presidents of institutes.