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Born in Bern. He studied in Zurich, Berlin, London and Vienna, obtaining his doctorate in Bern in 1865. From 1872 he succeeded Georg Albert Lucke as Ordinary Professor of Surgery and Director of the University Surgical Clinic at Berne. He published works on a number of subjects other than the thyroid gland including haemostasis, antiseptic treatments, surgical infectious diseases, on gunshot wounds, acute osteomyelitis, the theory of strangulated hernia, and abdominal surgery. His new ideas on the thyroid gland were initially controversial but his successful treatment of goitre with a steadily decreasing mortality rate soon won him recognition. The prize money for the Nobel helped establish the Kocher Institut in Berne.
A number of instruments and surgical techniques are named after him as well as the Kocher-Debre-Semelaigne syndrome.