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Born in Edinburgh in 1873, Balfour received his education at George Watson's College and at the University of Edinburgh where he graduated MB CM in 1894. After graduation he joined his father in general practice but it soon became clear that he was inclined toward preventive rather than curative medicine. He went to Cambridge University in 1895, taking his Diploma in Public Health in 1897. He returned to Edinburgh University where he graduated MD with a thesis on the toxicity of dyestuffs and river pollution for which he was awarded the Gold Medal. He took the Edinburgh BSc in Public Health at Edinburgh University in 1900 before serving as a civil surgeon in the Transvaal in the second Boer War, 1900-1901. On his return he became interested in tropical medicine through his friendship with Sir Patrick Manson and took a course at the School. In 1902 he was appointed Director of the Wellcome Tropical Research Laboratory at Khartoum and Medical Officer of Health to that city. He remained in Khartoum until 1913 and his work was published in four reports from the Wellcome Tropical Research Laboratories (1904-1911). On his return to England, he founded and directed the Wellcome Bureau of Scientific Research and organised what was to become the Wellcome Museum of Medical Science. He made an extensive tour of South America and the West Indies. He took on many different roles during World War One, at the outbreak he was in uniform in France, in 1915 he became a temporary Lt Col, Royal Army Medical Corps. In 1915-1916 he became a member of the Medical Advisory Committee, Mediterranean Expeditionary Force, he was the President of the Medical Advisory Committee, Mesopotamia 1916-1917, Scientific Adviser to Inspecting Surgeon-General, British Expeditionary Force, East Africa, 1917 and President of the Egyptian Public Health Commission, 1918.
He returned as Director in Chief of the Wellcome Bureau and became a member of the Colonial Advisory Medical and Sanitary Committee and Medical Research Committee. In 1921 he visited Mauritius to advise on sanitation and went to Bermuda in 1923 on a similar expedition. In 1923 he was appointed the first Director of the London School of Hygiene and Tropical Medicine. In 1926 he revisited the Sudan at the invitation of the Government, presided at the opening of the State Institute in Warsaw and gave an address at the opening of the School of Hygiene in John Hopkins University in America. He was elected President of the Royal Society of Tropical Medicine and Hygiene, 1925-1927, he became D.Sc and LL.D (Edinburgh) and LL.D of Johns Hopkins and Rochester Universities in USA and also a Fellow of the Royal College of Physicians of London and Edinburgh. In 1920 he received the Mary Kingsley Medal of the Liverpool School of Tropical Medicine. He was knighted in 1930. He died from a fall from a window of a nursing home in Kent on 1 January 1931. Selected publications include (medicine): Medicine, Public Health and Preventive Medicine (with C. J. Lewis, 1902); Memoranda on Medical Diseases in Tropical and Sub-Tropical Areas (1916); War Against Tropical Disease (1920); Reports to the Health Committee of the League of Nations on Tuberculosis and Sleeping Sickness in Equatorial Africa (1923); Health Problems of the Empire (with H. H. Scott, 1924); (novels/historical adventures): By Stroke of Sword (1897); To Arms (1898); Vengeance is Mine (1899); Cashiered and Other War Stories (1902); The Golden Kingdom (1903).