The rules governing discovery in a civil case are much broader. Under Federal Rule of Civil Procedure 26, either party can obtain information within discovery that “need not be admissible in evidence to be discoverable.” Mr. Balwani can depose potential witnesses, such as Theranos’s investors, who may also testify in the criminal case. That would give his defense a preview of what they might say at the criminal trial.

Judge Davila allowed federal prosecutors to ask for a stay in the S.E.C.’s case, but then rejected their argument that Mr. Balwani was misusing civil discovery to help him prepare for the criminal case. The judge quoted from a decision in the mid-1990s involving Charles Keating, who gained fame for his alleged looting of Lincoln Savings & Loan. In that case, the United States Court of Appeals for the Ninth Circuit stated that “in the absence of substantial prejudice to the rights of the parties involved, simultaneous parallel civil and criminal proceedings are unobjectionable under our jurisprudence.”

Because the S.E.C. filed its case first, and prosecutors did not ask for a stay when the criminal case began three months later, Judge Davila found that granting a stay might abridge Mr. Balwani’s “procedural and discovery rights.” The judge noted that the criminal case could end in a mistrial, with the jury unable to agree on whether to convict or acquit the defendants, a possibility that cuts against granting the Justice Department’s request to stay discovery in the civil case.

A key question in the civil case will be whether Mr. Balwani will assert his Fifth Amendment right against self-incrimination. Most defendants assert the privilege so that prosecutors cannot use the deposition testimony at trial. By opposing the Justice Department’s motion for a stay, Mr. Balwani effectively conceded that he may have to assert the privilege to avoid answering questions.

Doing so could be problematic for Mr. Balwani. The S.E.C. could use his refusal to testify as evidence that he was involved in misconduct. It would not necessarily prove fraud, but the jury can weigh it in deciding whether a defendant violated the law.

For Mr. Balwani, the benefits of pursuing civil discovery in the S.E.C. case appear to outweigh that risk. And if he has a joint defense agreement with Ms. Holmes, indicating that they will put up a united front in the criminal case, he may be able to share information from the civil case with her attorneys.

That could give the defense an advantage in the criminal prosecution.