The judge immediately said he would tell them to go back and deliberate some more.
Jurors gave no indication of what decision they had reached on the two counts where they did agree.
They said they have not discussed 11 counts of wire fraud, many of which involve telephone conversations that were taped by the FBI. Many of those discussions relate to the allegation that Blagojevich attempted to sell or trade President Barack Obama's old Senate seat.
The communication from jurors indicated that they have discussed the remaining 11 counts and appear to be deadlocked on them.
Blagojevich and his co-defendant brother listened intently, sitting at the edge of their chairs, as the presiding judge read the jury note. After the hearing adjourned, the ex-governor quickly smiled in a huddle with attorneys. He put his arms around his wife Patti's shoulder.
"I would be foolish to speculate what a jury will do," one of Blagojevich's attorneys, Sam Adam Sr., told reporters at the courthouse.
Legal analyst Terry Sullivan said the fact the jury has reached consensus on only two counts is "very good news for the defense so far."
But he said just because they haven't voted on 11 wire fraud counts doesn't mean they haven't considered them because the alleged acts of wire fraud are part of the first count, racketeering.
"They had to have at least considered mail and wire fraud," Sullivan, a Chicago attorney and former prosecutor, said in an interview on WGN-TV.
The jury had sent a note to Judge James B. Zagel on Wednesday saying they were stuck, but without giving specifics. Zagel had asked for clarification, and said Thursday he wants the jury to go back and discuss the wire fraud counts.
Blagojevich, 53, has pleaded not guilty to charges including that he tried to sell or trade the Senate seat appointment for a Cabinet post, private job or campaign cash and tried to leverage the power of his office for personal gain. If convicted, he could face up to $6 million in fines and a sentence of 415 years in prison, though he is sure to get much less time under federal guidelines.
His brother, Tennessee businessman Robert Blagojevich, 54, faces four counts and has pleaded not guilty.
Judges have a lot of autonomy about what to do in case of deadlock over some or all counts, said Michael Helfand, a Chicago attorney with no link to the case.
Besides sending them back to keep trying, a judge can ask jurors if there's anything he could provide that might help them reach a verdict - for instance, transcripts of specific witness testimony. They haven't had any transcripts of testimony during their deliberations to date.
Zagel praised the Blagojevich jurors on Wednesday, calling them disciplined and diligent. Any discord has apparently been civil, Zagel told the court, with no reports of shouting or screaming from the 25th floor jury room where the 12 jurors gather each weekday. "Jurors have a hard, thankless job - and you very rarely see a judge that doesn't treat jurors as well as possible," Helfand said. "So the fact Zagel praises them, won't mean he'll let them off the hook."
If jurors are deadlocked on most counts, prosecutors could retry Blagojevich on counts where the jury couldn't agree, said Helfand. He said that's likely, especially if there's deadlock on the most important charges, like racketeering.