The validity of 46 patent court judges’ rulings are now under fire, thanks to the efforts of a George Washington University law professor that discovered a constitutional flaw in the process that appoints them.

“I actually ran [my discovery] by a number of colleagues who teach administrative law and constitutional law,” said Professor John F. Duffy. “No one thought it was a close question.”

Since 2000, says Duffy, patent judges have been appointed by the Secretary of Commerce. However, the Constitution restricts the appointment of inferior officers – of which patent judges are classified – to the President, “Courts of Law,” or government department heads.

The director of the Patent and Trademark Office previously held appointment duties, before a 1999 law shifted the burden to the Secretary of Commerce. Since then, 46 of the 74 judges that sit on the Board of Patent Appeals and Interferences (BPAI) were elected under the new law.

“That method of appointment is almost certainly unconstitutional,” writes Duffy (PDF).

According to the New York Times, the Justice Department has done everything but admit that Duffy is right: DoJ lawyers warned that Duffy’s discovery could be “cataclysmic” for the patent world, flinging open the doors for a bonanza of appeals and decision challenges. Such a finding would “cast a cloud over many thousands of board decisions … unsettling the expectations of patent holders and licensees across the nation.”

Compounding the problem is the sheer amount of money involved: patent judges over see cases with millions of dollars at stake, adjudicating over things like who invented something first, or challenges to a declined patent. One tech firm, Translogic, currently has $86 million on the line as it asked the Supreme Court to consider such a question last month.

Constitutional problems with pending legislation are overseen by the Justice Department’s Office of Legal Counsel, but it is overwhelmed with work. John O. McGlinnis, the former deputy assistant attorney general at the Office of Legal Counsel from 1987 to 1991, notes that the O.L.C. sees “an enormous number of bills.”

“A line attorney might just miss it,” he said.

Manipulation of governmental appointments was one of the United States founders’ “greatest grievances against executive power,” wrote Justice Harry A. Blackmun in his ruling for Freytag v. Commissioner, one of the precedent cases in Duffy’s and Translogic’s question. Limiting appointment power ensures that those appointed “were accountable to political force and the will of the people.”