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A federal judge unsealed grand jury testimony Friday in which Barry Bonds insisted he had never knowingly used banned drugs even when confronted with documents indicating he had tested positive for steroids.

The contents of Bonds’ 2003 testimony from the BALCO steroids scandal were first reported by the Chronicle in 2004, but the transcript itself had never been made available to the public.

At a hearing in U.S. District Court in San Francisco, Judge Susan Illston ordered the transcript unsealed, saying it was germane to Bonds’ upcoming trial on perjury and obstruction-of-justice charges.

The original indictment revealed Bonds had tested positive for testosterone in an independent test sought by BALCO’s Victor Conte in November 2000. The document released Friday shows that prosecutors questioned Bonds about what appeared to be at least one other test, from Jan. 19, 2001, revealing an elevated testosterone level.

In Bonds’ indictment, the government said it had evidence of multiple occasions on which Bonds had tested positive for steroids. A source familiar with the case said that Conte had made a practice of “pre-testing” elite athletes whom he was supplying with steroids, tracking how they were being affected by their drug regimens. The Bonds positives were from such pre-tests, the source said.

Also at the hearing, the judge told federal prosecutors they had improperly drafted Bonds’ indictment, in which he was accused of repeatedly lying under oath about using banned drugs supplied by BALCO.

Before the prosecution of the former Giants star can go forward, the government must either rewrite the indictment, which charged Bonds with four counts of perjury and one count of obstruction of justice, or file a new one, the judge said. She set another hearing on the matter for March 21.

The unsealed transcript gives a detailed account of Bonds’ Dec. 4, 2003, appearance before a grand jury that was investigating both BALCO officials and Bonds’ personal trainer, Greg Anderson, on suspicion of distributing undetectable steroids called “the cream” and “the clear.”

During Bonds’ three hours on the witness stand, prosecutors confronted the slugger with what they said were incriminating documents seized in raids on BALCO and on Anderson’s home in 2003.

Prosecutors said the documents detailed Bonds’ use of a long list of drugs: human growth hormone, Depo-Testosterone, “the cream” and “the clear,” insulin and even Clomid, a female fertility drug. The documents, many with Bonds’ name or initials on them, are dated from 2001 through 2003.

Prosecutors queried Bonds closely about them, but he denied using the drugs and said he had never seen the documents before.

At one point, prosecutor Jeff Nedrow showed Bonds the results of a steroid screen ordered in November 2000 by Conte. Nedrow said the tested urine sample belonged to Bonds, and he noted that the report showed Bonds had elevated levels for the injectable steroid nandrolone and for methenolone, a steroid available in both injectable and oral form.

“I got to ask, Mr. Bonds,” the prosecutor said. “There’s this number on a document with your name … and it does have these two listed anabolic steroids as testing positive in connection with it. Do you follow my question?”

Bonds replied, “I follow where you’re going, yeah.”

The prosecutor continued, “I guess I got to ask the question again. I mean, did you take steroids? And specifically this test is in November of 2000. So I’m going to ask you in the weeks and months leading up to November, 2000, were you taking steroids?”

“No,” Bonds replied.

The prosecutors said other test reports also showed elevated levels of testosterone, but Bonds resolutely denied using steroids.