Werner Zimmerli studied medicine in Basel University, Switzerland, and obtained the PhD in 1974. After continuous education in inner medicine and rheumatology, he worked in a research project at the Department of Infectious Diseases in Geneva. The project aimed to explain high susceptibility to infection of implants lead by the pathogen mechanisms. Afterwards he worked as a chief and consulting physician in Infectious Diseases department in University Hospital Basel. This was followed by examination of function of granulocytes (tutored by John Gallin) during his research stay at the National Institutes of Health in Bethesda/USA. In 1989 he completed his habilitation in internal medicine and became a professor at the University of Basel in 1992. From 1991 till 1999 he led the newly established department of Infectious Diseases at the University Hospital Basel. In 1999 he began to work as a professor and a chief physician in inner medicine at Medical University Clinic Liestal.
Since 1979 his research focus was pathophysiology and treatment of implant infections. A major breakthrough in the treatment of such infections was the proof of the effectiveness of rifampicin against biofilm infections. Together with Peter Ochsner, an orthopedic surgeon, who worked in the same hospital in the field of orthopedic infections, and infectious diseases specialist Andrej Trampuz, he developed a treatment algorithm for patients with periprosthetic infections, which was published in N Engl J Med. Werner Zimmerli was a member of Infectious Diseases Society of America (IDSA), which published guidelines for diagnosis and treatment of prosthetic infections. The guidelines are based on published therapy algorithm and apply today as an international standard.
Since his retirement as chief medical doctor, Werner Zimmerli continues to work as a consultant professor in orthopedic infections at the Medical University Clinic Liestal.