He was born at Leith, Midlothian to Robert Middleton, a customs collector of Bo'ness, Linlithgowshire, and Helen, daughter of Captain Charles Dundas RN and granddaughter of Sir James Dundas of Arniston.
Seton suffered great hardships at the hands of the rebels during the English Civil War, and his father had to sell family estates long held in Linlithgowshire, that of Niddry Castle and one at Winchburgh, to rescue him from imprisonment.
His father having died, young Lauder was also forfeited, in 1337, of his paternal inheritance: the lands of "Balmegon" (Balgone), "Balnegog", Wester Crag Craig, Garvald, Fanulton (Fenton), Newhall, Popil, all in Haddingtonshire, and lastly Auldcathy in Linlithgowshire.