Born in Lanarkshire 27 Oct 1761, the son of Rev James Baillie (subsequently professor of divinity at the University of Glasgow) and Dorothea Hunter, sister of William and John Hunter. His sister was poet Joanna Baillie. Educated at Hamilton. Student at University of Glasgow and Balliol College, University of Oxford from 1779. Graduated AB 1783, AM 1786, MB 1786, MD 1789.
Baillie spent his holidays in London staying with his uncle William Hunter, and studied anatomy at St George's under his uncle John Hunter, as well as assisting him on his lectures and demonstrations and supervised students making dissections. On the death of William Hunter, Baillie inherited £5,000, Hunter's house on Great Windmill Street and the use of Hunter's museum until 30 years from Hunter's death, as well as a small estate in Scotland, which he gave to John Hunter. Baillie lectured at the school from 1783-84 to 1799 or 1803.
He was appointed physician at St George's Hospital in 1787. Candidate of the Royal College of Physicians 1789, fellow 1790; censor in 1791 and 1796, elect 1809. Honorary fellow of the Royal College of Physicians in Edinburgh 1809. Fellow of the Royal Society. Baillie succeeded his friends David Pitcairn and Dr Warren to practice, which grew so rapidly that he resigned his appointment at St George's as well as giving up on teaching anatomy, devoting himself to his medical practice. Appointed physician extraordinary to George III and in 1814 physician in ordinary to Princess Charlotte. Declined baronetcy for his services to the king.
Published widely on anatomy and pathology; his 'The Morbid Anatomy of Some of the Most Important Parts of the Human Body', published in 1793, is considered the first systematic study of pathology, and the first publication in English on pathology as a separate subjects. He is credited with identifying transposition of the great vessels (TGV) and situs inversus.
Married Sophia Denman, daughter of physician Thomas Denman, an alumnus of St George's. Retired to Gloucestershire, where he died 23 Sep 1823, aged 62 after briefly suffering from inflammation of the mucous membrane of the trachea. His wife Sophia died in 1845, aged 74.