The decision is not because of the Boy Scouts’ policies on LGBT inclusion, the church said in a statement. “The BSA has always allowed the Church to operate its programs in ways that are consistent with our standards and beliefs, and they have been very supportive.”

Instead, the church said simply that the teen programs have been “historically difficult to implement within the Church,” while Cub Scouts and Boy Scouts “currently meet the development program needs of boys from ages 8 through 13.” The church will instead create its own youth programs for teenage boys.

Effie Delimarkos, a spokeswoman for Boy Scouts of America, said that 130,000 boys ages 14 to 18 participate in Varsity and Venturing through Mormon Church troops, making up more than 5 percent of the Boy Scouts’ 2.3 million youth members. The Mormon Church is the Boy Scouts’ largest partner — about 20 percent of Boy Scouts are Mormon.

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“We’re sad to see that decision, but we understand,” Delimarkos said. She attributed the church’s move not to sexuality issues but to the church’s desire for a Mormon youth program more focused on preparing teenage boys to go on church missions.

“We’re just not kind of aligning with what the church needs men to focus on,” she said.

Church spokesman Eric Hawkins said no leaders of the church would discuss the decision with a reporter. But he said that leaving Varsity and Venturing could offer the church a chance to test its own youth programming and that it may someday leave the Boy Scouts altogether.

The Boy Scouts began admitting gay Scouts in 2013 and transgender Scouts this year, and the Mormon Church has not objected to either decision. Who can lead a Scout troop has been a more controversial question.

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In 2015, facing a lawsuit, the Boy Scouts lifted its ban on gay men leading Scout troops. The LDS church reacted immediately with a statement that it was “deeply troubled” and that “the century-long association with Scouting will need to be examined.”

A few weeks later, the church said that it would stick with the Boy Scouts for the time being but would “continue to evaluate and refine program options that better meet its global needs.” Thursday’s announcement about the teen programs was the first decision to come out of that evaluation.

Hawkins said the church wants to eventually pick a youth program in which all Mormons worldwide, not just Americans and Canadians, can participate.

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“They’ve been very open about the necessity for a program that would serve global needs,” Delimarkos said. “We know that there’s an interest there. That being said, we know that there’s strength in the Cub Scout and Boy Scout programs, and they see value in it. We certainly hope that they continue to stay with Cub Scouts and Boy Scouts.”

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The Mormon Church runs its own program for teen girls, and families had complained that it is not as well funded as the boys’ activities. On Thursday, the church said the new program that will replace Varsity and Venturing will correct that spending imbalance.

Although the church will withdraw from Varsity and Venturing at the beginning of 2018, it said it will pay the same registration fees through the end of that year to ease the effect on the Boy Scouts. The church will also continue to support all teenage Mormons who want to become Eagle Scouts, the prestigious rank associated with the Boy Scouts.

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The church’s withdrawal may affect the future of the programs themselves. The Venturing program is used in other churches and secular organizations, Delimarkos said — and unlike Cub Scouts or Boy Scouts, Venturing includes both boys and girls in non-Mormon troops. But Varsity, which the Mormon Church used for its 14- and 15-year-olds, was largely developed in conjunction with the church and used by Mormon troops. Boy Scouts may consider altering the program now, Delimarkos said.

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Other religious groups have also distanced themselves from Scouting because of unease about LGBT inclusion and other social issues — most recently, the Archdiocese of Kansas City in Kansas told its churches to disband all their Girl Scout troops. Meanwhile, Scout troops remain popular not just in churches, but in some synagogues and mosques.