Gillies was born in Dunedin, New Zealand. He studied medicine at Gonville and Caius College, Cambridge University, where despite a stiff elbow (sustained sliding down the banisters at home as a child) he was a rowing blue. Gillies married Kathleen Margaret Jackson on November 9, 1911, in London. They had four children. His youngest son Michael Thomas Gillies followed his father into medicine.
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