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The Sternberg peer review controversy concerns the conflict arising from the publication of an article supporting pseudoscientific intelligent design creationism in a scientific journal, and the subsequent questions of whether proper editorial procedures had been followed and whether it was properly peer reviewed. One of the primary criticisms of the intelligent design movement is that there are no research papers supporting their positions in peer reviewed scientific journals. On 4 August 2004, an article by Stephen C. Meyer (Director of Discovery Institute's Center for Science and Culture) titled "The origin of biological information and the higher taxonomic categories", appeared in the peer reviewed journal, Proceedings of the Biological Society of Washington. Meyer's article was a literature review article, and contained no new primary scholarship itself on the topic of intelligent design. The following month, the publisher of the journal, the Council of the Biological Society of Washington, released a statement repudiating the article and stating that their former editor Richard M. Sternberg had, in an unusual manner, handled the entire review process without consultation or review from an associate editor. The same statement from the Council vowed that proper review procedures would be followed in the future and endorsed a resolution published by the American Association for the Advancement of Science, which states that there is no credible scientific evidence supporting intelligent design. On September 18, the Discovery Institute issued a statement praising the publication of Meyer's paper in a peer reviewed journal and chastising the National Center for Science Education for stating that the paper should not have been published. The Biological Society of Washington's president, Roy McDiarmid called Sternberg's decision to publish Meyer's article "a really bad judgment call on the editor's part" and said it was doubtful whether the three scientists who peer reviewed the article and recommended it for publication were evolutionary biologists. The event has been used to support an unsubstantiated but common narrative of persecution. on the phylogeny of crabs. In February 2001 he began work as an invertebrate taxonomist for the National Institutes of Health at the National Center for Biotechnology Information, later becoming a staff scientist. The position allowed time for research work, and he continued at the NMNH, now as an unpaid research associate. Soon after starting work, he agreed to take on the unpaid position of Managing Editor of the peer reviewed scientific journal, Proceedings of the Biological Society of Washington, Around this time he was sympathetic to historic ideas of structuralism of patterns in nature, but could not go from that to inferring the existence of a designer. He occasionally met proponents of intelligent design, and in 2002 presented a lecture on formal causation to the ISCID intelligent design group's "Research And Progress in Intelligent Design" (RAPID) conference. In October 2003 Sternberg resigned from being editor of the Proceedings of the Biological Society of Washington, with a commitment to edit issues over the coming year. Early in 2004 intelligent design advocate Stephen C. Meyer contacted Sternberg about a manuscript that he was thinking of submitting to the journal. Sternberg advised him he would have to become a member of the Society, and in a few weeks Meyer sent him copies of the manuscript with evidence of membership. Sternberg went ahead with the review and editing process, He subscribes to the process structuralism school of thought. In 2005 he said he was not a proponent of intelligent design. He has more recently described his position as one that "can accept all that is empirically valid in evolutionary biology, while not axiomatically dismissing the position that structures as well as their "real" instantiations have an intelligent cause", and asserts that the universe emanates from Nous (mind), so that his thinking "is compatible with intelligent design broadly defined." He is also a signatory to the Discovery Institute's Scientific Dissent from Darwinism petition.

In a review of Meyer's article The origin of biological information and the higher taxonomic categories, Alan Gishlick, Nick Matzke, and Wesley R. Elsberry claimed it contained poor scholarship, that it failed to cite and specifically rebut the actual data supporting evolution, and "constructed a rhetorical edifice out of omission of relevant facts, selective quoting, bad analogies, knocking down straw men, and tendentious interpretations." Critics of Sternberg believe that he was biased in the matter, arguing that Sternberg's close personal and ideological connections to the paper's author suggest at least the appearance of conflict of interest. They cite as evidence Sternberg's presentation in 2002 of a lecture on intelligent design at the Research And Progress in Intelligent Design (RAPID) conference where Stephen C. Meyer, the author of the paper Sternberg published, also presented a lecture. The explicit purpose of the RAPID conference was to "form new collaborations among scientists seeking to do research on the interface between science and faith, particularly within the context of ID". Only intelligent design advocates spoke at it, and at least one intelligent design critic was expressly forbidden to attend it. It was organized and hosted by the International Society for Complexity, Information and Design (ISCID), a group dedicated to promoting intelligent design, of which Sternberg is a Fellow. ISCID is affiliated with the Discovery Institute, hub of the intelligent design movement, where Meyer serves as the Program Director of the Center for Science and Culture. Critics also note that Sternberg also sat on the editorial board of the Baraminology Study Group, Critics describe Sternberg's explanation of events, that a pro intelligent design paper just happened to find its way to a publication with a sympathetic editor ultimately responsible for ensuring proper peer review and editing of his last issue, and that he decided it was appropriate to deal with the review process in person on a subject in which he has a personal interest, as improbable and that "people who want us to believe that the publication process outlined [by Sternberg and his defenders] was transparent and only had to do with science" are "disingenuous."

After the peer review controversy became public, Sternberg filed a religious discrimination complaint against the Smithsonian Institution's National Museum of Natural History, where he had an unpaid appointment as a research associate, while employed by the National Institutes of Health. Sternberg claims that he was "targeted for retaliation and harassment" and subject to efforts to remove him from the museum in retaliation for his views in support of intelligent design. He continues to cite a letter by the United States Office of Special Counsel as supporting his version of events, despite the fact that the Office of Special Counsel did not proceed beyond its initial investigation. In its initial investigation, Office of Special Counsel concluded that there was a strategy by several managers to force Sternberg out of the Smithsonian Institution and that there was a strong religious and political component to the actions taken after the publication of the Meyer article. For example, one of the emails sent between Smithsonian employees stated, "Scientists have been perfectly willing to let these people alone in their churches, but now it looks like these people are coming out and invading our schools, biology classes, museums and now our professional journals. These people to my mind are only a scale up on the fundies of a more destructive kind in other parts of the world. Depressing. Oh, if we only still had Steve Gould to lead the counter attack". Pim Van Meurs and other critics observed that the Office of Special Counsel lacked jurisdiction over the matter and so his claim was unlikely to proceed, and that even though it made no official findings or conclusions, the response from the Office of Special Counsel provided Sternberg and the Discovery Institute putative evidence and talking points supporting their claim that the scientific community discriminates against intelligent design proponents. In a Wall Street Journal op ed article, Discovery Institute Senior Fellow David Klinghoffer portrayed Sternberg as a martyr and victim of discrimination, a tactic used often by design proponents. In response, Sternberg's supervisor at the Smithsonian, Jonathan Coddington, responded publicly disputing Sternberg's and Klinghoffer's depiction of events. Coddington states that Sternberg was never dismissed, nor was he a paid employee, and that he was never the target of discrimination, and remained serving at the museum up to that time. In a November 2005 National Public Radio report on the affair, Sternberg stated "I'm not an evangelical, I'm not a fundamentalist, I'm not a young earth creationist, I'm not a theistic evolutionist". Sternberg said McVay "related to me, 'the Smithsonian Institution's reaction to your publishing the Meyer article was far worse than you imagined'." Barbara Bradley Hagerty, NPR's religion reporter, said Sternberg himself believes intelligent design is "fatally flawed." In December 2006 a partisan report was issued by Mark Souder, on the basis of information he and fellow Republican representative and intelligent design advocate Rick Santorum (author of the pro ID Santorum Amendment) had requested, calling into question the Smithsonian's treatment of Sternberg and repeating many of Sternberg's claims. The report was commissioned by Souder in his capacity as subcommittee chairman of the House of Representatives Committee on Government Reform, written by his subcommittee staff, but published by Souder as an individual representative without it being officially accepted into the Congressional Record. This is contrary to oft repeated claims by the Discovery Institute and other design proponents that the report represents an official position by the Committee supporting Sternberg's claims of discrimination. Observers have said that facts of the case simply do not support the conclusions of the report nor is the report an official report of the committee. They say that the Discovery Institute is using the report to portray Sternberg specifically, and design proponents in general, as victims of persecution. They also say the Souder report is a repackaging of the Office of Special Council's previous findings from August 2005 and contains nothing new, consisting of "the OSC findings restated and used as a form of evidence in and of themselves" and attacks the Smithsonian for "not accepting the OSC's findings at face value." They cite as evidence of a biased motive behind the report the longstanding connections of the report's instigators, Congressmen Souder and Santorum, to the Discovery Institute, whose Program Director is Stephen C. Meyer, author of the paper Sternberg published. In 2000 Souder co hosted a congressional briefing on behalf of the Discovery Institute intended to drum up political support for intelligent design and read a defense of intelligent design prepared by the Discovery Institute into the congressional record. The April 2008 film featuring Ben Stein promoting intelligent design, Expelled: No Intelligence Allowed, included interviews with Sternberg and claims that his "life was ruined". Both Scientific American and the National Center for Science Education state that the film misrepresents key facts.