WASHINGTON — With two short answers, Andy Pettitte called into question the validity of his testimony against Roger Clemens, part of a discouraging day for prosecutors in the retrial of the seven-time Cy Young Award winner.

After stumbling its way to a mistrial of Clemens last year, the government is struggling again in the retrial — to the point that the crux of Pettitte’s testimony might be tossed out. First, the exasperated judge criticized the questioning of Pettitte on Wednesday, then he ruled against prosecutors in another matter. Finally he cried out: “You’re taking positions that are totally absurd to me.”

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Former Major League Baseball pitcher Roger Clemens, center, leaves federal court on Tuesday in Washington. AP

Pettitte, Clemens’ longtime friend and former teammate, was on the stand for a second day in the trial that is to determine whether Clemens lied at a 2008 congressional deposition and hearing when he denied taking steroids and human growth hormone.

During cross-examination, Clemens’ lawyers got exactly the answers they wanted.

Might Pettitte have misunderstood when Clemens supposedly acknowledged using human growth hormone to Pettitte in a conversation during the 1999-2000 offseason?

“I could have,” Pettitte answered.

Is it fair to say there is a “50-50” chance that Pettitte misunderstood?

“I’d say that’s fair,” Pettitte replied.

The government tried to salvage their witness, but prosecutor Steven Durham’s follow-up questions were lacking — at least in the minds of Clemens’ lawyers and, more importantly, U.S. District Judge Reggie Walton. Clemens’ lawyers moved to strike Pettitte’s testimony about the 1999-2000 conversation as “insufficiently definitive.”

The judge seemed to agree, openly wondering why Pettitte wasn’t asked for a current, definitive recollection of the conversation. He repeatedly berated Durham, who was also part of the government team last July when prosecutors showed the jury a snippet of inadmissible videotaped evidence, prompting the mistrial.

“I was waiting for you to ask, and you didn’t ask that,” Walton said.

“My understanding is that (Pettitte’s) position is at this time, he is conflicted. … His testimony now before the jury is ‘I don’t know,'” the judge continued. “I thought that what we would hear is, ‘Mr. Pettitte, currently, what is your memory of what Mr. Clemens told you back in 1999?'”

In other words, the jury might have concluded that maybe Pettitte did “misremember” the conversation, as Clemens has claimed.

Durham tried to contend that he addressed the matter in a different way. The defense will file a brief in support of its position, and Walton could rule on Pettitte’s testimony as early as Thursday.

During his first day on the stand Tuesday, Pettitte recalled the crucial conversation, which took place at Clemens’ home during a workout, as: “Roger had mentioned to me that he had taken HGH.” Pettitte’s testimony — as a reluctant witness with no ulterior motive — is considered vital for the prosecution’s case, which otherwise relies heavily on Brian McNamee, a former strength coach for both Pettitte and Clemens who says he injected Clemens with steroids and human growth hormone.

After his testimony, Pettitte signed a baseball in the hallway and left the courthouse in a black SUV without commenting, free to continue his comeback with the New York Yankees.

Inside, the government’s woes continued. Its next witness wasn’t even allowed to take the stand.

Prosecutors had planned to call Steve Fehr, an attorney for the Major League Baseball players’ union. Fehr was supposed to help show, in an indirect manner, that Clemens was aware that former Sen. George Mitchell had tried to contact Clemens when putting together the 2007 Mitchell Report on drug use in baseball. Clemens was named in the report, prompting Congress to call the February 2008 hearing at which Clemens testified.

Walton said he didn’t understand what Fehr’s testimony would accomplish and that it could amount to “trampling on the attorney-client privilege” because it relies on Fehr’s conversations with Clemens’ lawyers. Walton said the government should use other evidence to show that Clemens was aware of the Mitchell request.

“Maybe I’m dense,” Walton said, his voice rising. “I’m starting to think that maybe I just don’t understand the law — because you’re taking positions that are totally absurd to me.”

The government kept trying to argue its case, but Walton would have none of it.

“You’re beating a dead horse, and you’re not going to make it come alive,” Walton said. “You’re not going to win this one.”

Nevertheless, Walton said he would allow the government to do some research and file a brief before making a final decision.

Prosecutors did get a minor victory later in the day when the judge allowed them to address in slightly greater detail the overall problem of performance-enhancing drug use in baseball to support Congress’ involvement in the matter. Clemens’ lawyers contend the 2008 hearing was a “show trial” of Clemens and not meant to serve a legislative purpose.

Therefore, with Fehr not allowed to take the stand, the government brought back congressional staffer Phil Barnett, whose testimony was interrupted Tuesday by Pettitte’s arrival as a witness from out of town. Barnett mentioned former major league stars Rafael Palmeiro and Chuck Knoblauch for the first time as players who have been associated with performance-enhancing drug use.

The day ended with jurors seeing photos of needles, gauze and other materials that McNamee says he used while injecting Clemens. They were shown during testimony from federal agent Jeff Novitzky, who helped spearhead drugs-in-sports investigations — including those of baseball’s Barry Bonds and star cyclist Lance Armstrong — first while working for the Internal Revenue Service and now at the Food and Drug Administration. Clemens’ lawyers are expected to claim the evidence has been tainted.

Novitzky will return to the stand Thursday.

In a behind-the-scenes move, McNamee filed a motion to quash a subpoena served by the defense on his ex-wife for records from their contentious divorce proceedings two years ago. The defense wants the records about McNamee’s past to attack his credibility. There was no indication when the judge would rule on McNamee’s request.

Clemens and Pettitte arrived at opposite ends of the courthouse a few minutes apart Wednesday morning, both in gray suits. Pettitte carried a backpack and a bottle of water.

During breaks when the judge and lawyers haggled over legal procedures, Pettitte looked down or straight ahead, never in Clemens’ direction. Clearly uneasy over testifying about his friend, he looked as if he couldn’t wait for it all to end.

Pettitte’s hedging on the conversation shouldn’t have come as a complete surprise to prosecutors. Back in his 2008 deposition, he mentioned a few times he might have misunderstood Clemens. At one point, under prodding from a congressional investigator, Pettitte said, “I don’t think I misunderstood him,” but even then added, “six years later when he told me that I did misunderstand him, you know, since ’05 to this day, you know, I kind of felt that I might have misunderstood him.”