Jurors in the James “Whitey” Bulger case were sent home this afternoon without reaching a verdict in the federal racketeering trial of the notorious South Boston gangster.

US District Court Judge Denise J. Casper dismissed the 12 jurors around 4:30 p.m., putting an end to their first full day of deliberations. Since getting the case Tuesday, jurors have deliberated for about 13 hours. They are due to resume at 9 a.m. Thursday.

“Jurors, we’re going to send you home for the day,’’ Casper told them in the Moakley Courthouse in South Boston.

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The jurors are weighing 32 counts against Bulger that allege that he participated in a racketeering enterprise that raked in millions of dollars from drug trafficking and the extortion of bookmakers, drug dealers, and businessmen. The indictment also alleges Bulger, who was a prized informant for the FBI, was responsible for 19 murders.

A mystery suddenly enshrouded the trial at midday. Prosecutors, defense attorneys, and the judge held animated discussions but would not say publicly what issue they were confronting.

“It’s frustrating,” said Patricia Donhaue, whose husband was allegedly murdered by Bulger. “All this secrecy.’’

The unexplained incident started around noon and lasted into the afternoon. Twice, lawyers and prosecutors suddenly gathered in Casper’s courtroom, huddled with her at sidebar, argued some points out of hearing of the public, and then left.

The lawyers said they could not say what was discussed because the conversation was held at sidebar, where issues the judge wants to keep away from the jury are usually discussed.

But after the second meeting with the judge ended around 2:30 p.m., Assistant US Attorney Brian Kelly told relatives of Bulger’s alleged victims that the jury would continue to deliberate.

“Now we wait,’’ Kelly told relatives.

While the lawyers talked with the judge, Bulger sat at the defendant’s table looking like he was in a library, scribbling notes on a scrap of yellow paper with his glasses on. Sitting in the area reserved for relatives of the defendant were several of the adult children of Bulger’s brother, William, the former president of the Massachusetts Senate and former president of the University of Massachusetts.

Earlier today, jurors asked Casper whether they should be concerned about the statute of limitations affecting some of the charges against Bulger, who rampaged through Boston’s underworld from the 1970s to the 1990s.

But Casper told them that all of the charges before them were brought within the applicable statute of limitations. “So you do not have to concern yourself with statute of limitations as to any charges or counts,” she said.

The charges go years into the past because Bulger slipped away from law enforcement in 1994 and successfully eluded a worldwide manhunt for more than 16 years, until he was captured in seaside Santa Monica, Calif., in 2011.

Casper also provided each of the 12 jurors with a printed copy of the entire legal instructions she gave them Tuesday before they began deliberations in the high-profile trial of the 83-year-old Bulger.

Casper addressed the jurors after they sent her a series of questions around 10 a.m. today, about an hour after they began their closed-door deliberations in the federal courthouse in South Boston. The judge referred the jury to the pages of her instructions that defined the elements of murder, joint venture, and aiding and abetting

On Tuesday, the jury of four women and eight men spent 5 ½ hours sifting through evidence presented over the past eight weeks before adjourning around 4:30 p.m. Among the exhibit available to them are charts of Boston’s gangland hierarchy, gruesome crime scene photos, and stacks of FBI informant reports.

The names of the jurors have not been made public, but the man selected as the foreman told Casper during the selection process that he was a stay-at-home father who recently got a part-time job at a bank. He also told her that his wife was concerned he would lose the job if chosen, but Casper kept him in the pool, and now he is directing the jury’s deliberations.

Casper told jurors during a one-hour-and-40-minute instruction on the law Tuesday that they must reach a unanimous verdict on every count and all of the acts listed in the racketeering count.

Jurors heard 35 days of testimony from 72 witnesses, including three of Bulger’s closest former associates: Stephen “The Rifleman” Flemmi, Kevin Weeks, and John Martorano, who admitted their own involvement in murders and were given controversial plea deals in exchange for their cooperation with authorities against Bulger and corrupt FBI officials. The jury also heard from a corrupt FBI supervisor, John Morris, who admitted taking $7,000 in bribes from Bulger and Flemmi and leaking information to them.

Prosecutors presented evidence that Bulger was an FBI informant from 1975 to 1990 and that his corrupt handler, John J. Connolly Jr., leaked information that allegedly prompted Bulger and his associates to kill three FBI informants who were cooperating against them, an innocent bystander, and a potential witness.

The defense essentially put the government on trial as it focused on FBI corruption and argued that Bulger was never an informant, but rather paid agents for information. The defense also repeatedly pressed its assertion that Flemmi, not Bulger, killed two women, Debra Davis and Deborah Hussey, who are the only women among Bulger’s 19 alleged victims.

Bulger has pleaded not guilty to all charges and is being held without bail.