Inspired by Pasteur, who claimed on the basis of experimentation that fermentation and putrefaction were caused by minute living organisms in the atmosphere, 'germs', Lister reasoned that if microbes could cause infection, they could be killed before reaching the open wound. His use of carbolic acid on dressings and instruments, as well as on surgeons and patients, resulted in stunning results. The mortality rate among his amputee cases fell from 45 percent to 15 percent.

In 1867, Lister published a series of papers in the Lancet describing his system of antiseptic surgery. Lister proposed a chemical barrier between the wound and the atmosphere in the form of carbolic acid, which Lister introduced into the wound with an additional layer of carbolic soaked lint. In the first series of Lancet papers, Lister reported on eleven cases of compound fractures of which nine recovered.

He continued throughout his working life to experiment with other chemical antiseptics, with carbolic sprays for the surgical environment, with appropriate dressings, and to argue for medical practice based upon experimental procedures.

Lister retired in 1892, by a man honoured for his contribution to medicine in 1883 by a baronetcy and later, in 1897, by a peerage (Baron Lister of Lyme Regis) and, in 1902, by the Order of Merit.