Two years before he was admitted to the Incorporation, but some time after he had completed his apprenticeship to David Pringle, John Baillie was commissioned in the 3rd Foot Guards (Scots Guards) which were quartered in Edinburgh from 1679.
Being an army surgeon does not seem to have prevented him from participating fully in the affairs of the Incorporation or the town. In 1685 he was elected by the Burgh Council as one of the visitors for the Apothecaries to inspect their shops ‘for purging them of rotten and insufficient drugs’. Two of the Town Councillors opposed his appointment declaring ‘that they wold not vott for a Chirurgeon apothecarie to be ane of the visetors’. The opposition probably stemmed from the newly created Royal College of Physicians (1681) which saw inspection of the apothecaries as their prerogative.
Baillie was Deacon or President in modern terminology of the Incorporation from 1687 to 1689. His re-election in 1688 was postponed because of the troubled state of the country. The Town Council had some involvement in the election of the Deacons of all the guilds but in September 1688 the Council decided to hold no further meetings until 10th October ‘in respect of the present juncture of affairs anent the Hollanders' invasion’ and the local militia were called out. The election of Deacons, normally held at Michaelmas (September 29), was postponed.
The Town Council minutes of October 1688 note that Baillie was ‘presently out of the Kingdom on His Majesty's Service'. Thomas Edgar, the past Deacon, was appointed to officiate until he returned. In fact he was in England with the Foot Guards one battalion of which went to London and one to Salisbury with King James VII. William of Orange landed in England at Torbay on 5th November 1688 and the Scots Guards went over to his side. At some time in his army career Baillie is thought to have served in Flanders.
He was involved in treating the Lord President of the Court of Session, the supreme court in Scotland, in 1689. He was on hand when the Right Honourable Sir George Lockhart was shot. He probed the wound but the musket ball had entered at the back exiting at the right breast and Lockhart died. The murderer was John Chiesly of Dalry who was first tortured to find out if he had any accomplices and then sentenced to have his right hand cut off prior to being hanged.
In 1702 Baillie conducted the second day of the public anatomy demonstration which followed the opening of the new Anatomy Theatre when he discoursed on ‘the peritoneum, omentum, stomach, intestines, mesentery and pancreas’.
He taught 14 apprentices in all and employed a total of 13 servants. Four of the servants became apprentices, and two of the combined number became master surgeons. One of these was David Fyfe, who began as Baillie's servant in 1686, was apprenticed in 1688 and entered the Incorporation in 1695. Fyfe, in his turn, took on eight apprentices and 13 servants.
