Like many members of the Incorporation towards the end of the 17th century, Gideon Eliot had received his initial medical degree in Lyden. Much of his surgical experience was gained as a military surgeon in an era dominated by conflicts.
Gideon Eliot studied medicine at Lyden, matriculating in 1686. He was admitted to the Incorporation 3 years later.
In that same year he became surgeon to the Cameronians. This regiment had been raised in May 1689, largely to protect the Covenanters, Scottish Presbyterians who supported the National Covenant of 1638. This had been signed by many Scots opposed to the Kings determination to impose an episcopal system of religion in Scotland, with the King effectively as its head. In 1685 Covenanting was declared to be treason, punishable by death and the Covenanters were forced to hold services in secret - hence the need for protection by soldiers.
Gideon Eliot was surgeon to the Cameronians. Their first major battle was at Dunkeld where they defeated the much larger army of Stewart sympathisers, making the end of what was effectively the first Jacobite uprising. Eliot attended to the wounded at this battle.
He was elected Deacon of the Incorporation in 1694 and 95. On 3 April that year he was asked, along with the physician Sir Thomas Burnett, by King William to visit the Earl of Home who was under house arrest at Hirsel near Coldstream. They were required to report on whether the Earl was fit to be transferred for imprisonment in Edinburgh Castle. For this service Sir Thomas, as the King's Physician received £200 while Eliot received only £100. Hirsel near Coldstream remains to this day the Seat of the Earls of Home.