In this capacity he began to give lectures at his house in Bartholomew Close, which were so well attended that the governors of the hospital built a theatre (1790–1791), and Abernethy thus became the founder of the medical school of St Bartholomew's. He held the office of assistant-surgeon for twenty-eight years, till, in 1815, he was elected principal surgeon. He had before that time been appointed lecturer in anatomy to the Royal College of Surgeons (1814). Abernethy was not a great operator, though his name is associated with the treatment of aneurysm by ligature of the external iliac artery.