Specialist Jeremy Hall, 23, outside Fort Riley, Kan., where he has been stationed since being sent home early from Iraq because of threats from fellow soldiers.

NYT / ED ZURGA

FORT RILEY, Kan. — When Specialist Jeremy Hall held a meeting last July for atheists and freethinkers at Camp Speicher in Iraq, he was excited, he said, to see an officer attending.

But minutes into the talk, the officer, Maj. Freddy J. Welborn, began to berate Hall and another soldier about atheism, Hall wrote in a sworn statement. “People like you are not holding up the Constitution and are going against what the Founding Fathers, who were Christians, wanted for America!” Welborn said, according to the statement.

Welborn told the soldiers he might bar them from re-enlistment and bring charges against them, according to the statement.

Last month, Hall and the Military Religious Freedom Foundation, an advocacy group, filed suit in federal court in Kansas, alleging that Hall’s right to be free from state endorsement of religion under the First Amendment had been violated and that he had faced retaliation for his views. In November, he was sent home early from Iraq because of threats from fellow soldiers.

Eileen Lainez, a spokeswoman for the Defense Department, declined to comment on the case, saying, “The department does not discuss pending litigation.”

Hall’s lawsuit is the latest incident to raise questions about the military’s religion guidelines. In 2005, the Air Force issued new regulations in response to complaints from cadets at the Air Force Academy that evangelical Christian officers used their positions to proselytize. In general, the armed forces have regulations, Lainez said, that respect “the rights of others to their own religious beliefs, including the right to hold no beliefs.”

To Hall and other critics of the military, the guidelines have done little to change a culture they say tilts heavily toward evangelical Christianity. Controversies have continued to flare, largely over tactics used by evangelicals to promote their faith. Perhaps the highest profile incident involved seven officers, including four generals, who appeared, in uniform and in violation of military regulations, in a 2006 fundraising video for the Christian Embassy, an evangelical Bible study group.

“They don’t trust you because they think you are unreliable and might break, since you don’t have God to rely on,” Hall said of those who proselytize in the military. “The message is, ‘It’s a Christian nation, and you need to recognize that.’ ”

Soft-spoken and younger looking than his 23 years, Hall began a chapter of the Military Association of Atheists and Freethinkers at Camp Speicher, near Tikrit, to support others like him.

At the July meeting, Welborn told the soldiers they had disgraced those who had died for the Constitution, Hall said. When he finished, Welborn said, according to the statement: “I love you guys; I just want the best for you. One day you will see the truth and know what I mean.”

Welborn declined to comment beyond saying, “I’d love to tell my side of the story because it’s such a false story.”

But Timothy Feary, a soldier who attended the meeting, said in an e-mail message: “Jeremy is telling the truth. I was there and witnessed everything.”

It is unclear how widespread religious discrimination or proselytizing is in the armed forces, constitutional law experts and leaders of veterans’ groups said. No one has independently studied the issue, and service members are reluctant to come forward because of possible backlash, those experts said.

There are 1.36 million active duty service members, according to the Pentagon, and since 2005, it has received 50 formal complaints of religious discrimination, Lainez said.

In an e-mail statement, Bill Carr, the Defense Department’s deputy under secretary for military personnel policy, said he “saw near universal compliance with the department’s policy.”

But Mikey Weinstein, a retired Air Force judge advocate general and founder of the Military Religious Freedom Foundation, said the official statistics masked the great number of those who do not report violations for fear of retribution.

Since the Air Force Academy scandal began in 2004, Weinstein said, he has been contacted by more than 5,500 service members and, occasionally, military families about incidents of religious discrimination. He said 96 percent of the complainants were Christians, and the majority of those were Protestants.

Complaints include prayers “in Jesus’ name” at mandatory functions, which violates military regulations, and officers proselytizing subordinates to be “born again.” After getting the complainants’ unit and command information, Weinstein said, he calls his contacts in the military to try to correct the situation.

“Religion is inextricably intertwined with their jobs,” Weinstein said. “You’re promoted by who you pray with.”

After his run-in with Welborn, Hall did not file a complaint with the Army’s Equal Opportunity Office because, he said, he was mistrustful of his superior officers. Instead, he told leaders of the Military Association of Atheists and Freethinkers, who put him in touch with Weinstein. Though with a different unit now at Fort Riley, Hall said the backlash had continued. He has a no-contact order with a sergeant who, without provocation, threatened to “bust him in the mouth.” Another sergeant allegedly told Hall that as an atheist, he was not entitled to religious freedom because he had no religion.

Responding to questions about Hall’s experience at Fort Riley, the staff judge advocate, Col. Arnold Scott, said in an e-mail message, “In accordance with Army policy, Fort Riley is committed to ensuring the rights of all its soldiers are protected, including those of Specialist Hall.”

Civilian courts in the past have been reluctant to take on military cases, and the Justice Department has yet to respond to Hall’s lawsuit.

“Even if it doesn’t go through, I stood up,” Hall said. “I don’t think it is futile.”