 It was his intention during the visit to Paris to undergo an operation for the stone, but bad health prevented him from making the journey, and in February 1598 he resigned the office of secretary of state.He died at Balcarres, Fife, 3 September 1598, and in accordance with his Will he was buried in the parish kirk of Kilconquhar.By his first wife, Marion, daughter of Alexander Guthrie, town clerk of Edinburgh, and widow of David Borthwick of Lokhill, lord advocate, he had two sons—John, lord Menmuir, who died unmarried in January 1601, and David Lindsay, 1st Lord Balcarres—and three daughters