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St George's Tron Church said it had taken the decision after more than 12 months of thought and prayer.
Last year, the Kirk's General Assembly voted to accept gay clergy provided they had declared their sexuality and were ordained before 2009.
The 500-strong St George's Tron congregation believes this decision "has marginalized the Bible".
The decision to formally secede from the Church of Scotland was taken by the congregation on Monday.
read more: http://www.bbc.co.uk/news/uk-scotland-glasgow-west-18441172