When it comes to deciding whether to preside at same-sex marriages, military chaplains will be relying on their personal conscience and matters of faith instead of new Pentagon guidelines that allow them to do so.

A week ago, the Pentagon issued new directives that allow military chaplains to perform same-sex marriages at military facilities in states that allow such unions.  Same-sex marriages are legal in Connecticut, Iowa, Massachusetts, New Hampshire, New York, Vermont and the District of Columbia.

According to a memo detailing the change,  military chaplains  are not required to officiate at such ceremonies if “doing so would be in variance with the tenets of his or her religion or personal beliefs.”

The almost 2,700 chaplains who serve in the military represent a broad spectrum of religious faiths, including Buddhism, Islam, Judaism and many Christian denominations.   They also minister to the spiritual needs of service members of all faiths beyond the ones in which they are ordained.

The guidelines have created a political backlash. House Armed Services Committee Chairman Buck McKeon, R-Calif., said this weekend that he will oppose passage of the annual defense authorization bill  unless language is included that prohibits military chaplains from performing same-sex unions.

However,  military chaplains contacted by ABC News say whatever decisions they make about performing such unions will depend less on the political arena and more on religious principles and personal conscience.

“The Pentagon can issue a policy change concerning the performance of same-gender ceremonies by chaplains.  However, the Pentagon doesn’t generate religion as such,” says Gary Pollitt, a spokesman for the Military Chaplains Association, which represents 1,600 current and retired military chaplains.

In an e-mail statement he adds, “A military chaplain conducts religious ceremonies and rites in keeping with the canons [or beliefs, doctrine, policies] of the religious faith group that endorses that chaplain.  Each faith group defines the parameters for religious rites and the clergyperson’s individual discretion [if any] with those rites. ”

The United Churches of Christ is one of the few Christian denominations that allows its ministers to perform same-sex marriages or blessings of same-sex unions in the states that allow them.

Rev. Stephen Boyd, the Minister of Government and Professional Chaplaincies for the United Churches of Christ, says the 55 to 60 military chaplains from his denomination will use their personal conscience to help them decide whether to perform a sex-same marriage for a service member..

However, Boyd says any service member who wishes to have a military chaplain perform a same-sex marriage will bear the responsibility for finding a military chaplain willing to preside over such a ceremony.

“They have the responsibility to find those chaplains,” Boyd says.  “They can’t expect every chaplain to do this carte blanche … but those chaplains are there” says Boyd.

The Episcopalian Church allows its ministers to bless same-sex unions, but they cannot perform same-sex marriages because the church does not recognize marriage between people of the same gender. Bishop Jay Magness, the Episcopalian Suffragan of the Armed Services and Federal Ministries, says it will be up to individual military chaplains in his ministry to decide whether they feel comfortable with blessing a same-sex union.

“I don’t expect them to do that or not to do that. That s up to their personal conscience,” says Magness, who adds that his main concern is that anyone who comes to one of his chaplains with  a request to bless a union ” be treated with respect and dignity.”

In cases where an Episcopalian military  chaplain refuses to bless a union, he expects them to “do everything they can to find another chaplain … within the same faith or any faith ” who is willing to do so.

“We have a right and a responsibility to provide for everyone in the Armed Forces whether they are gay, straight, or whether they are Christian or non-Christian, ” says Magness.

Most Christian denominations define marriage as a union between a man and a woman.  In the wake of the Pentagon’s new guidelines, some religious leaders overseeing military chaplains have reaffirmed their denomination’s opposition to the practice of same sex marriage.

In a statement, Catholic Archbishop Timothy P. Broglio of the Archdiocese for the Military Services  maintained that the new directives  appear “to ignore the Defense of Marriage Act (DOMA), which was signed into law 15 years ago and remains in effect.”

Broglio added that the Pentagon “cannot say, on the one hand, that chaplains may take part in any private ceremony as long as it is ‘not prohibited by applicable state and local law,’ and on the other, say nothing of the federal law.”

The new guidelines would allow for same-sex ceremonies at multi-denominational chapels in states like New York that allow same-sex marriage.  Unlike most military facilities that have multi-denominational chapels, the U.S. Military Academy at West Point, N.Y., has chapels dedicated to individual faiths.  A spokesman for the Catholic Archdiocese of the Military Services says that in keeping with Catholic canon, the Catholic chapel at West Point will not be made available for such ceremonies.

It remains unclear what kind of an impact the Pentagon’s new guidelines will have on same sex marriages at military facilities.

“Within the first days we haven’t heard of any personal stories good or bad about the memos on the chaplains and their abilities to perform ceremonies but we do think that this is a positive thing and will allow for religious freedom and equality,” said Paul Guequierre,  a spokesman for the Human Rights Campaign.

Boyd says that in the end, the new guidelines will have a minimal impact on the military and won’t create much of a backlash. Like the repeal of “don’t ask, don’t tell,” it will create an initial flashpoint that will ultimately involve “certain men and women who take this union seriously,” he says.  And because only six states allow gay marriages, Boyd  says the new guidelines are “only going to  be very minimal on its impact in the military, I think.”