Gilchrist fathered a number of children during his time in India between 1782 and 1804. However, their legitimacy and the identity of the mother are unclear, and it appears that several died young. One surviving daughter, Mary Anne (b. 1786), may have remained in India after Gilchrist departed and it is known that, in 1810, she married Major Charles William Burton in Calcutta. He was the son of James Burton, canon of Christ Church, Oxford and chaplain to George III and George IV. Charles William Burton died at Mirzapur in 1816 and decades later, his and Mary Anne's son, Major Charles Aeneas Burton, was murdered together with his two sons at Kotah in 1857, during the Indian mutiny.