Clemens, the All-Star pitcher and seven-time Cy Young Award winner, maintains he has never used steroids or other performance-enhancing drugs. His former personal trainer, Brian McNamee, claims otherwise, testifying that he injected Clemens with human growth hormones and steroids at least 16 to 21 times from 1998 to 2001.
FBI agents in Washington opened the case a little more than two weeks after both Clemens and McNamee appeared at the same House hearing on Feb. 13, each accusing the other of lying.
"The request to open an investigation on the congressional testimony of Roger Clemens has been turned over to the FBI and will receive appropriate investigative action by the Washington Field Office," said FBI spokeswoman Debra Weierman.
CBS News legal analyst Andrew Cohen wonders whether the matter is it will take to investigate.
"Does our embattled Justice Department have anything better to do in the spring of 2008 than to prove that Roger Clemens was (or was not) injecting something into his butt (or having his trainer do it)?" asks Cohen.
The inquiry came on the heels of a request Wednesday from the House Oversight Committee, could result in perjury or obstruction of justice charges against Clemens. Lawmakers did not ask for a similar investigation of McNamee.
Clemens was first identified as taking steroids in a December report by former Senate Democratic Leader George Mitchell, who looked at drug use in baseball. The Mitchell Report was the first public accounting of McNamee's allegations that he injected Clemens with HGH and steroids.
Two of Clemens' former New York Yankees teammates, Andy Pettitte and Chuck Knoblauch, have both acknowledged that McNamee was correct when he said they used performance enhancers.
In a letter seeking the inquiry, the House panel cited sworn statements by Pettitte to bolster suspicion of Clemens' statements during the committee hearing.
"We believe that his testimony in a sworn deposition on Feb. 5, 2008, and at a hearing on Feb. 13, 2008, that he never used anabolic steroids or human growth hormone, warrants further investigation," House Oversight Committee Chairman Henry Waxman of California and ranking Republican Tom Davis of Virginia wrote.
"That testimony is directly contradicted by the sworn testimony of Brian McNamee, who testified that he personally injected Mr. Clemens with anabolic steroids and human growth hormone," the lawmakers wrote.
"Mr. Clemens's testimony is also contradicted by the sworn deposition testimony and affidavit submitted to the committee by Andrew Pettitte, a former teammate of Mr. Clemens, whose testimony and affidavit reported that Mr. Clemens had admitted to him in 1999 or 2000 that he had taken human growth hormone."
Clemens is the latest professional athlete to come under federal scrutiny for statements made about alleged use of steroids or performance-enhancing drugs. Last month, the FBI opened an investigation into whether Houston Astros shortstop Miguel Tejada lied when he told federal authorities he never took steroids or HGH.
Additionally, former Olympic track gold medalist Marion Jones was sentenced in January to six months in prison for lying to federal investigators about taking the designer steroid "the clear." The drug has been linked to the Bay Area Laboratory Co-Operative, the lab at the center of the steroids scandal in professional sports.