WASHINGTON - A federal judge has denied class certification in an antitrust case against Whole Foods Market Inc., striking a blow to the 2008 lawsuit brought by an unhappy customer concerned about rising prices.

The case is an offshoot of the Federal Trade Commission’s 2007 challenge to Whole Foods’ merger with former competitor Wild Oats. In October 2008, in light of the commission’s case, California resident Ekaterini Kottaras filed a civil antitrust lawsuit of her own against Whole Foods in U.S. District Court for the District of Columbia.

Ms. Kottaras moved to certify a class in January 2010. Although she had originally sued on behalf of Whole Foods customers nationwide, alleging that the merger made it possible for the company to hike up prices, her motion would have certified a class of consumers at 20 stores in Los Angeles County.

District Judge James Boasberg on Jan. 30 found that because proposed class members would need to present evidence that would vary from person to person, certifying a class would be inappropriate. He found that Ms. Kottaras’ expert failed to present a workable model for accurately determining any net damages to Whole Foods customers and that, even if he had, each class members’ potential damages would depend on what they bought.

“Since the collection of products purchased by a particular customer is only provable by individual evidence…it would be impossible to establish ‘widespread injury’ or even determine who belongs in the class, with common proof,” Judge Boasberg wrote in Kottaras v. Whole Foods Markets Inc., 08-cv-01832.

Lead counsel for Whole Foods, Dechert’s Paul Denis, wrote in an e-mail that “We are pleased with the Court’s decision which is grounded in a clear understanding of the facts, the expert testimony and the law.” Dechert attorneys Christine Levin, Sean Pugh and Carolyn Budzinski are also working on the case.

Ms. Kottaras is being represented by Roy Katriel of The Katriel Law Firm in Washington and Michael Braun of Braun Law Group in Los Angeles. Neither returned a request for comment.

Ms. Kottaras, like the FTC, was concerned that the merger would create monopolies in areas where Whole Foods and Wild Oats were the only stores of their kind—premium, natural, and organic supermarkets. One of these markets was in Los Angeles County, where Kottaras lives.

Whole Foods has 13 stores in the New York metropolitan area.

District Judge Paul Friedman had originally denied the commission’s motion for a preliminary injunction, finding that the FTC offered too narrow a market definition and that there was no evidence the merger would lessen competition. He was reversed by a 2008 ruling from the U.S. Court of Appeals for the D.C. Circuit.

That case eventually settled in 2009, with Whole Foods agreeing to divest 32 stores from the merger agreement. Ms. Kottaras’ case, which Judge Friedman was also presiding over at the time, was held up that year by a fight over a subpoena from her attorneys for Whole Foods to turn over documents submitted by third-party supermarkets in the FTC case.

The case was reassigned in July to Judge Boasberg. He heard oral arguments on the motion to certify a class in December. A status hearing is scheduled for Feb. 13.