Controversy and division were common in the Church between 1750 and 1850, when there was considerable concern about the Church's relations with the State, particularly over intervention in the appointment of ministers. The largest division was the Disruption of 1843 - a major split which saw about one third of the Kirk break away to form what came to be the Free Kirk.

The next 90 years were spent removing the causes of division, and reuniting several churches, all of them presbyterian, so that today the Church of Scotland is the largest Protestant church in the country, with a number of very small churches alongside it, representing those who chose not to find their way into the union process.