Baillie was born at Glasgow, the son of Baillie of Jerviston. Having graduated there in 1620, he gave himself to the study of divinity. In 1631, after Baillie was ordained into the Church of Scotland, acting for some years as regent in the university, he was appointed to the living of Kilwinning in Ayrshire. His abilities soon made him a leading man. In 1638 he was a member of the Glasgow Assembly, when Presbyterianism was re-established in Scotland, and soon after he accompanied Leslie and the Scottish army as chaplain or preacher. In 1642, Baillie was made Professor of Divinity, Glasgow, and in the following year was selected as one of the five Scottish clergymen who were sent to the Westminster Assembly. In 1649, he was one of the commissioners sent to Holland for the purpose of inviting Charles II to Scotland, and of settling the terms of his admission to the government. He continued to take an active part in all the minor disputes of the church. In 1651, he was made professor of divinity in Glasgow University, and in 1661 was made principal. He died in August of the following year, his death likely hastened by his mortification at the apparently firm establishment of episcopacy in Scotland.

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