[3] He was forfeited for treason by Regent Moray in Parliament in Edinburgh on 19 August 1568 for his support of Mary, Queen of Scots, after her escape from Lochleven Castle, having fought for her at the battle of Langside.
[4] In July 1570, he was accused with Claud Hamilton and others, of making plans to ambush Regent Lennox and the Earl of Mar in Callender Wood.
[5] John Hamilton, Archbishop of St Andrews denied his own involvement in this plan during his trial in April 1571.
[6] In March 1575 Andrew's brother, John Hamilton, was among the Hamiltons who made peace with Regent Morton on the issue of a murder in March 1575 at Holyroodhouse, after handing their swords to the Captain of Edinburgh Castle, George Douglas of Parkhead.
On 18 May 1579, Sir James Hamilton younger (of Libberton) helped the King's forces take Craignethan Castle.