Among the most damaging leaks was a secret recording the Chronicle described in an October published report. A voice the Chronicle claimed to be Anderson's was heard saying he provided steroids to Bonds.

The U.S. Attorney on the case has asked the Department of Justice to investigate the leak. Once again, the Government investigates itself.

CrimProf Blog thinks either the defense or a government employee leaked the transcript. I rule out the defense. The Chronicle in discussing its decision to release the information, gives away a big clue:

Here is how we decided to publish secret testimony: We don't believe that it's our responsibility to enforce federal secrecy provisions surrounding grand jury proceedings.

Under federal law, only prosecutors, case agents, government and court employees and others on that side of the fence are prohibited from disclosing matters that occur before the grand jury. The defense is under no such prohibition. If a person associated with the defense had been the source, there would be no federal secrecy provision for the Chronicle to consider enforcing.

That leaves the Government, case agents and persons working for them. Why doesn't the Judge just call all of them into chambers, put them under oath, and ask if they were the source of the leak or if they know who was? They will know that if the leaker ever surfaces elsewhere, and they lied to the judge, they will face perjury charges as well as obstruction charges and lose their jobs. One of them might just cave under such pressure. Who should the Judge call? I'd start with these people, all listed in the Department of Justice press release on the Indictment:

The prosecution is the result of an 18-month investigation overseen by the U.S. Attorney's Office as well as special agents of the Internal Revenue Service Criminal Investigation Division, the Food and Drug Administration Office of Criminal Investigations and the San Mateo County Narcotics Task Force. In addition, the Bureau of Immigration and Customs Enforcement provided assistance in connection with the investigation. Jeff Nedrow is the Assistant U.S. Attorney who is prosecuting the case with the assistance of Susan Kreider.

The Balco Indictment is here (pdf.)

Update: I would just like to point out that if a defendant had received grand jury transcripts from the Government as part of discovery in his criminal case, which would only happen after indictment, and the Court issued an order preventing the defense from sharing them with anyone outside the defense team, it would be a violation for the defense to have provided them to the Chronicle.