He met Dr. Robin Warren, a pathologist interested in gastritis, during internal medicine fellowship training at Royal Perth Hospital in 1981.

"[12] On the other hand, it has also been argued that medical researchers showed a proper degree of scientific scepticism until the H. pylori hypothesis could be supported by evidence.

Due to other hospital work, the lab technicians did not have time to immediately throw out the 31st test on the second day, and so it stayed from Thursday through to the following Monday.

They later found out that H. pylori grows more slowly than the conventional two days required by other mucosal bacteria, and that stomach cultures were not contaminated by other organisms.

[14] In 1983 they submitted their findings thus far to the Gastroenterological Society of Australia, but the reviewers turned their paper down, rating it in the bottom 10% of those they received that year.

[14] After failed attempts to infect piglets in 1984, Marshall, after having a baseline endoscopy done, drank a broth containing cultured H. pylori, expecting to develop, perhaps years later, an ulcer.

Marshall's illness and recovery, based on a culture of organisms extracted from a patient, fulfilled Koch's postulates for H. pylori and gastritis, but not for peptic ulcers.

[22] He established the Noisy Guts Project in 2017 – a research team dedicated to investigating new diagnostics and treatments for Irritable Bowel Syndrome.

In August 2020, Marshall, along with Simon J. Thorpe, accepted a position at the scientific advisory board of Brainchip INC, a computer chip company.

[24] In 2005, the Karolinska Institute in Stockholm awarded the Nobel Prize in Physiology or Medicine to Marshall and Robin Warren, his long-time collaborator, "for their discovery of the bacterium Helicobacter pylori and its role in gastritis and peptic ulcer disease".

In 1985, Marshall showed by self-administration that this bacterium, now called Helicobacter pylori, causes acute gastritis and suggested that chronic colonisation directly leads to peptic ulceration.