As a medical student, Martin Arrowsmith (Ronald Colman) approaches the revered Professor Gottlieb (A. E. Anson) wishing to accelerate his studies into bacteriology research. Gottlieb insists that he complete his clinical training first. But Arrowsmith meets the cheeky nurse Leora (Helen Hayes) and throws over his plans for science in order to earn a marriage-sustaining living as a general practitioner in her native South Dakota.

Assuaging his undying passion for research (in the family kitchen), he takes on the problem of an epidemic of black leg disease of cattle and earns the animus of a veterinarian and the admiration of the Swedish farmers by single-handedly disproving the efficacy of a government serum, developing his own serum, and conducting a controlled trial to prove its worth. His frustrated and unemployed wife--now displaced from her own kitchen--continues to support him, answering always "Yes, Martin. No, Martin. Whatever you say, Martin."

The couple move to New York City where Arrowsmith intends to devote himself full time to science at the side of his old hero Gottlieb in the McGurk Institute (a thinly disguised Rockefeller Institute). In his new laboratory, Arrowsmith utters a prayer for clear vision and humility--a prayer that seems to go unanswered.

Late one snowy night after two years of fruitless work, he discovers that "something" (in the novel, it is bacteriophage) has killed the bacteria he has been incubating. "Is it important, Martin?" asks Leora. He is brutal in his zealous response, his eyes gleaming with the promise of promotion, fame, and fortune. But after days of exhausting labour, he learns that he has been scooped by Felix D’Herelle a (real) researcher at the Pasteur Institute.

Arrowsmith quickly finds a new passion and travels to the Caribbean to conduct research into the effect of a serum on bubonic plague. Gottlieb makes him promise to act like a scientist (not a G.P. or a quack) and to withhold the remedy from half his patients. He tries to convince the colonial authorities of the importance of controlled testing, but is rebuffed with accusations of turning humans into guinea pigs. A black medical graduate of Howard University invites him to a different island where the epidemic is so thick that the people willingly cooperate with the controlled trial.

Leora, who had refused to remain in New York, is now left behind. The film implies clumsily that the now solitary Arrowsmith--ecstatic to be back in the research trenches--has a romantic encounter with Joyce, a beautiful stranded tourist (Myrna Loy). Meanwhile, Leora contracts plague from a cigarette, which has absorbed plague germs from Martin’s sloppy lab technique, and which she smokes because of Martin’s inattention and abandonment. She dies miserably and alone.

Crazed with remorse, Arrowsmith abandons his scientific principles and allows the entire population to be treated with the serum after all. The epidemic is arrested. But Martin knows that his success does not justify his scientific sin. Still grieving for Leora, he returns to New York to much fanfare, but is unable to find absolution from Gottlieb who has just had a stroke. He runs out on his lover, his institute, and a press conference to join a friend who is establishing a Walden-like institute dedicated to pure research in Vermont.