Some Southern Baptists have said that the Baptist World Alliance had adopted liberal theology and "anti-American'' thinking.
The pullout was approved overwhelmingly by a show of hands.
"Each organization is independent. If a church still wants to go and join it, they can do so. They are supported individually. It is just that we are not supporting anymore as a denomination," said the Rev. Michael Hail of Perry, Fla.
"Our goal seems to have gone in different directions. We are very conservative and they have become more liberal and as you know our Southern Baptist Convention is very conservative," said Brenda Marten, a delegate from South Carolina.
"I think that it has to do with some homosexual issues that Southern Baptists believe the Bible is very clear on, that some denominations are adopting a more 'who should have a will, let them come.' Which is true, but in a leadership capacity, there are some in the scripture that limits that," said Fort Wayne, Ind., delegate Anthony Payton.
The SBC is the world's largest Baptist denomination and America's largest Protestant body, with over 16 million members.
The Falls Church, Virginia-based alliance is a federation of 46 million Baptists in 211 denominations.
The SBC pullout means the loss of a third of its income base.
Network News Service contributed to this report.