Long a lightning rod for conservative criticism, the Girl Scouts of the USA are now facing their highest-level challenge yet: An official inquiry by the U.S. Conference of Catholic Bishops.

At issue are concerns about program materials that some Catholics find offensive, as well as assertions that the Scouts associate with other groups espousing stances that conflict with church teaching. The Scouts, who have numerous parish-sponsored troops, deny many of the claims and defend their alliances.

The inquiry coincides with the Scouts’ 100th anniversary celebrations and follows a chain of other controversies.

Earlier this year, legislators in Indiana and Alaska publicly called the Scouts into question, and the organization was berated in a series aired by a Catholic broadcast network. Last year, the Scouts angered some conservatives by accepting into a Colorado troop a 7-year-old transgender child who was born a boy but was being raised as a girl.

Some of the concerns raised by Catholic critics are recycled complaints that have been denied by the Girl Scouts’ head office repeatedly and categorically. It says it has no partnership with Planned Parenthood, and does not take positions on sexuality, birth control and abortion. “It’s been hard to get the message out there as to what is true when distortions get repeated over and over,” said Gladys Padro-Soler, the Girl Scouts’ director of inclusive membership strategies.

In other instances, the scouts have modified materials that drew complaints – for example, dropping some references to playwright Josefina Lopez because one of her plays, “Simply Maria,” was viewed by critics as mocking the Catholic faith.

The new inquiry will be conducted by the bishops’ Committee on Laity, Marriage, Family Life and Youth. It will look into the Scouts’ “possible problematic relationships with other organizations” and various “problematic” program materials, according to a letter sent by the committee chairman, Bishop Kevin Rhoades of Fort Wayne, Ind., to his fellow bishops.

The bishops’ conference provided a copy of the letter to The Associated Press, but otherwise declined comment.

Girl Scout leaders hope the bishops’ apprehensions will be eased once they gather information. But there’s frustration within the iconic youth organization – known for its inclusiveness and cookie sales – that it has become such an ideological target, with the girls sometimes caught in the political crossfire.

“I know we’re a big part of the culture wars,” said the Girl Scouts’ spokeswoman, Michelle Tompkins. “People use our good name to advance their own agenda. “For us, there’s an overarching sadness to it,” Tompkins added. “We’re just trying to further girls’ leadership.”

With the bishops now getting involved, the stakes are high. The Girl Scouts estimate that one-fourth of their 2.3 million youth members are Catholic, and any significant exodus would be a blow given that membership already is down from a peak of more than 3 million several decades ago.

The inquiry coincides with a broader effort by the bishops to analyze church ties with outside groups. Rhoades’ committee plans to consult with Girl Scouts leaders and with the National Federation for Catholic Youth Ministry.

The federation’s executive director, Bob McCarty, praised the Girl Scouts for willingness to change some program content. “I don’t think any of this material was intentionally mean-spirited,” McCarty said. “I think a lot of it was lack of attention.”

However, McCarty expressed doubt that the Girl Scouts’ most vehement critics would be satisfied regardless of what steps are taken.Mary Rice Hasson, a visiting fellow in Catholic studies at the Ethics and Public Policy Center, a conservative think tank in Washington, accuses McCarty of “whitewashing” Girl Scout programs and policies that struck some Catholics as counter to church teaching.

“They just repeated the Girl Scouts’ denials,” Hasson said. “Families’ concerns were minimized or ignored.”

Hasson is pleased that the bishops are launching their own inquiry but is skeptical that further rifts can be avoided.

“A collision course is probably a good description of where things are headed,” she said. “The leadership of the Girl Scouts is reflexively liberal. Their board is dominated by people whose views are antithetical to the teachings of the Catholic Church.”

One of the long-running concerns is the Girl Scouts’ membership in the 145-nation World Association of Girl Guides and Girl Scouts.

The association, known as WAGGGS, is on record as saying girls and young women “need an environment where they can freely and openly discuss issues of sex and sexuality.” It also has called for increased access to condoms to protect against sexually transmitted diseases.

Some critics want the Girl Scouts of the USA to pull out of the world group; the scouts aren’t budging.

“Our world is becoming smaller and our young people need to have those opportunities to engage with their peers from around the world,” said the Girl Scouts’ CEO, Anna Maria Chavez.

To the Girl Scouts, some of the attacks seem to be a form of guilt by association. Critics contend that Girl Scouts materials shouldn’t contain links to groups such as Doctors without Borders, the Sierra Club and Oxfam because they support family planning or emergency contraception.

The Girl Scouts’ website addresses some of the recurring criticisms. “Parents or guardians make all decisions regarding program participation that may be of a sensitive nature,” it says.

And although it’s a secular organization, the Girl Scouts embrace partnerships with religious groups. Scouts can earn a “My Promise, My Faith” pin for activities linked to their religious beliefs.

The Girl Scouts have been entangled in the culture wars as far back as the 1970s, when some conservatives became irked by the prominence of feminists such as Betty Friedan in the organization’s leadership.

In 1993, Christian conservatives were outraged when the Girl Scouts formalized a policy allowing girls to substitute another word for “God” – such as Allah or Buddha – in the Girl Scout promise.

Among the disgruntled was Patti Garibay, a troop leader in Cincinnati who’d raised three daughters as Girl Scouts. In 1995, she founded the American Heritage Girls, which calls itself a “Christ-centered” alternative and now claims 19,000 members in 45 states.

Garibay said many of the newest members are from Catholic families disenchanted with the Girl Scouts. American Heritage Girls signed a memorandum of mutual support in 2009 with the Boy Scouts of America, and some local units conduct joint activities. The Boy Scouts have no equivalent pact with the Girl Scouts.

“When you have a leadership brand like Girl Scouts, it’s natural that we would have some critics,” said Chavez. “We’re proud of our inclusive approach because that is what has always made this organization strong.”