In 1855 he discovered, after writing his first monograph on polyps, that benign and malign polypoid tumors of the colon were related. As a result, he recommended early treatment for the condition. While writing his numerous works, Billroth began to teach historical developments in surgery and became professor of surgery and director at the University of Zurich from 1860 to 1867. He then went to teach at the University of Vienna and became the head of The Second Surgical Clinic at the General Hospital.

Billroth studied the bacterial causes of wound fever and implemented antiseptic techniques in his surgical procedures. This application resulted in successfully performing many high-risk procedures. In 1867, Billroth described in a report the complete removal of a carcinomatous prostate. His success during surgeries led him to be the first surgeon to remove a section of the oesophagus and join the remaining parts together (1872), complete excision of a larynx (1873) and remove a rectal cancer. In 1881, Billroth successfully abstracted a cancer pylorus—an almost inconceivable procedure for his time.

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