Ussher's younger, and only surviving, brother, Ambrose, became a distinguished scholar of Arabic and Hebrew.
According to his chaplain and biographer, Nicholas Bernard, the elder brother was taught to read by two blind, spinster aunts.
Ussher resisted this pressure at a convocation in 1634, ensuring that the English Articles of Religion were adopted as well as the Irish articles, not instead of them, and that the Irish canons had to be redrafted based on the English ones rather than replaced by them.
Theologically, he was a Calvinist although on the matter of the atonement he was (somewhat privately) a hypothetical universalist.
He was a prolific scholar and church leader, who today is most famous for his identification of the genuine letters of the church father, Ignatius, and for his chronology that sought to establish the time and date of the creation as "the entrance of the night preceding the 23rd day of October...
In 1615, he was closely involved with the drawing up of the first confession of faith of the Church of Ireland. He became a national figure in Ireland, becoming Privy Councillor in 1623 and an increasingly substantial scholar.
In 1619 Ussher travelled to England, where he remained for two years. A noted collector of Irish manuscripts, he made them available for research to fellow-scholars such as his friend, Sir James Ware.
This begins: The religion of the papists is superstitious and idolatrous; their faith and doctrine erroneous and heretical; their church in respect of both, apostatical; to give them therefore a toleration, or to consent that they may freely exercise their religion, and profess their faith and doctrine, is a grievous sin.
The Judgement was not published until it was read out at the end of a series of sermons against the Graces given at Dublin in April 1627.
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His only child was Elizabeth (1619–93), who married Sir Timothy Tyrrell, of Oakley, Buckinghamshire. From 1623 until 1626 he was again in England and was excused from his episcopal duties to study church history.