He received his MBBS from the University of Adelaide, having completed his high school education at St Peter's College, Adelaide. In 1967 he was admitted into the Royal College of Pathologists of Australia and became a senior pathologist at the Royal Perth Hospital where he spent the majority of his career. With his colleague Barry J. Marshall, Dr. Warren proved that the bacterium is the cause of stomach ulcers. Dr. Warren helped develop a convenient diagnostic test (14C-urea breath-test) for detecting H. pylori in ulcer patients. In 2005, Drs. Warren and Marshall were awarded the Nobel Prize in Medicine.
He married Dr. Winifred Theresa Warren and together they had five children, from oldest to youngest, John, David, Patrick, Andrew and Rebecca. Dr. Winifred Warren went on to become an accomplished psychiatrist.
An Australian documentary was made in 2006 about Drs. Warren and Marshall's road to the Nobel Prize, called "The Winner's Guide to the Nobel Prize". He was made a Companion of the Order of Australia in 2005.