When most scholars have their grant applications rejected by the National Endowment for the Humanities, they shrug. Only a small minority of grants are approved, so there's no way any application can be a sure thing.

But what about an application that earns the top possible rating from every member of a peer review panel? When Marc Stein learned that his application had been rejected despite getting the best possible ratings, he started to investigate patterns at the NEH -- and they led him to give a scathing talk Saturday at the annual meeting of the American Historical Association questioning the fairness of the NEH in dealing with his grant and others having to do with gay studies.

Saying that it was time to "name names," Stein reviewed the results of his inquiry, quoting from peer review comments he obtained, and the comments he received from NEH program officers. Stein also conducted a review of NEH fellowships and research awards and found recent years in which few or none of the projects had words like "gay," "lesbian," "queer" or various other words in their titles -- even though such topics are quite common in the humanities. (He acknowledged that this was not a precise measure and that some scholars may be doing work on these issues and keeping those words out of project titles.)

Stein's talk, which he also published with more detail and footnotes online at the History News Network, was widely discussed at the history meeting, with other gay scholars saying that he had demonstrated that their work was being unfairly evaluated and excluded.

"It's absolutely appalling," said Leisa D. Meyer, chair of the AHA's Committee on Gay and Lesbian History and a professor of history and women's studies at the College of William and Mary. "It's really dangerous the way the NEH is held hostage."

In an interview Sunday, Erik Lokkesmoe, a spokesman for the endowment, said that Stein's assumptions were incorrect and that there was no bias against work in gay studies. "The only litmus test we have is excellence," he said, adding that he would encourage gay studies scholars to apply for NEH grants. His message to these scholars: "Please call our program officers. We welcome your applications. They will get full consideration."

One reason Stein's charges generated a lot of buzz at the history meeting is that he is a well respected scholar and his proposed topic concerned legal history (Constitutional law in fact), just the kind of work the NEH generally likes to support. Stein teaches history and is coordinator of the Sexuality Studies Program at York University, in Canada. He is the author of a book about gay Philadelphia and served as editor in chief of the three-volume Encyclopedia of Lesbian, Gay, Bisexual and Transgender History in America.

He applied in 2003 to the NEH for a project to be called "The U.S. Supreme Court's Sexual Revolution? 1965-1973." His thesis was a challenge to the conventional wisdom about the court during this period, which is seen by many as a time in which the justices expanded individual rights regarding sexuality. Stein proposed to compare a series of rulings -- on topics such as birth control, interracial marriage, abortion, obscenity and gay rights -- to show that the liberalism associated with the court was based on a "heteronormative supremacy" and did not go nearly as far as people believe.

When Stein's proposal was rejected, he didn't think much of it at first, but decided to take advantage of an offer in the rejection letter that he could seek copies of the evaluation letters for his project. When he did so, he found that the peer review panel had raved over his ideas. Comments such as "right on target," "ideal combination of solid research and a topic that has broad appeal" and "seems truly revisionary and significant" appeared in these reviews. Every panelist had ranked the proposal "excellent."

Stein said he assumed then that many projects had received such high rankings and that he lost out to equally highly judged proposals. But as he gathered more information, he found that while he was rejected, one project in American history that had failed to receive all "excellent" rankings had been approved for support. A recommendation to support his grant had been overturned by the NEH's council -- a presidentially appointed panel -- and by Bruce Cole, chairman of the NEH and the final arbiter on awards.

When Stein applied again, he received slightly lower ratings -- with questions being raised about whether he had a "personal agenda." Stein was told by the NEH that Cole had decided that the "the negative concerns outweighed the positive" with regard to his grant application -- and he was again rejected.

Somewhere in the process, Stein said, he appears to have been a victim of "flagging." That's the term for some grant applications being identified for particularly close scrutiny as they move up the chain for approval at the endowment. The Chronicle of Higher Education reported that Lynne V. Cheney, who led the endowment under President George H.W. Bush, had used flagging to limit support for projects that related to multiculturalism and that Cole had revived the practice under the second President Bush.

On Sunday, Lokkesmoe acknowledged that flagging is part of the process, but he stressed that Cole has followed the recommendations of staff members (who summarize the peer review panels) and the NEH's council almost all the time, using his veto power sparingly.

The peer review process is important but it is only one part of getting an NEH grant, Lokkesmoe said. "There are many criteria to look at on whether an application deserves to be funded," he said. Lokkesmoe said that confidentiality rules barred him from discussing the specifics of Stein's application but that bias against gay studies was not a factor and is not an issue at the endowment.

He noted that Cole is "not trying to fight the culture wars" and that the NEH has backed many grants that relate to diversity. Indeed Cole -- who taught art history and comparative literature at Indiana University before coming to the NEH -- is a well respected scholar and his relations with academic groups are much more friendly than Cheney's were during her tenure at the NEH. "It's a different time," Lokkesmoe said.

To Stein and others at the AHA meeting, however, the question remains about why proposals that go through a rigorous peer review process -- in which the NEH selects the members of peer review panels -- should be overturned by political appointees. At the AHA's business meeting, Stein's experience was cited as an example of what's wrong with the NEH and as an illustration of the thinking behind the AHA's statement last year on peer review.

It reads, in part: "Projects endorsed by peer review panels composed of competent, qualified, and unbiased reviewers that reflect a balance of perspectives should not be denied funding because of political, religious, or other biases of political appointees in the funding agencies."

Since the historians can't force the NEH to change its procedures, Stein cited his experience as an example of how to seek change. If you are rejected by the NEH, he urged the audience, get all the information you can, and if the results strike you as unfair, start sharing the information with others.