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Congregationalism is a form of church government, or polity, practiced by some Protestant Christian churches, whereby individual churches operate independently of each other and vary in ideology, theology, etc.
Congregationalism really took off with the Protestant Reformation (although the ideal had been promoted before that, largely as a reaction to repression by the Catholic Church). The movement is most prevalent in the United States, where it has a long tradition starting with the Puritans of New England.
The early Christian church is believed to have been highly decentralized and often housing disparate ideologies. Congregationalists aim to emulate this, believing it brings them closer to the "true" Christianity. This has not worked out very well, however, as a very large number of Congregationalist churches switched to Unitarianism in the 19th century.
 Cultural effects
Due to the independent nature of the congregations, moderation is unknown in churches that practice congregational government; congregationally governed churches range from wingnut Baptist outfits like Fred Phelps's church to the very liberal churches in the United Church of Christ, which have an impressive track record of participating in the forefront of many social equality movements (e.g., civil rights, gay rights). Many ordain women and support gay marriage.
Barack Obama's ex-church, Trinity United Church of Christ, is part of the American Congregationalist denomination.