"Is a personality disorder a disease of the mind as a matter of law?" the jurors asked the judge as they emerged from their deliberations for the first time.
Quebec Superior Court Justice Guy Cournoyer answered "yes" and told them no more before sending them back to deliberate further on Magnotta's fate.
They remained holed up and left without asking anything else. They will resume deliberating Thursday.
The accused has admitted to killing and dismembering Jun Lin in May 2012 but his lawyer argues he should be found not criminally responsible because he is schizophrenic and couldn't tell right from wrong at the time.
The judge had told the jurors in his instructions they should start their work by focusing on the not criminally responsible issue.
Cournoyer also said they would need to answer two questions for the mental disorder defence to be accepted. Firstly, is it more likely than not Magnotta was suffering from a mental disorder at the time of the offence? And secondly, did the disorder make him incapable of knowing the acts were wrong?
The Crown has argued the crimes were planned and deliberate and that the steps Magnotta took to hide his tracks and flee authorities were not consistent with someone suffering from a mental disorder.
Prosecutor Louis Bouthillier said Magnotta's schizophrenia was a misdiagnosis and that his medical problems and behaviour are likely the result of personality disorders.
The accused faces four other charges in the case: criminally harassing Prime Minister Stephen Harper and other members of Parliament; mailing obscene and indecent material; committing an indignity to a body; and publishing obscene materials.
The eight women and four men began deliberating Tuesday after hearing some 66 witnesses over the 40 days the trial sat.
They will have to consider hundreds of pages of medical files, expert reports and the physical evidence gathered in Montreal as well as Europe.
They must deliver five unanimous verdicts in the case.
Also on Wednesday, Bouthillier told the court a witness from Germany is requesting further reimbursements for having testified at the trial.
Frank Rubert housed Magnotta during his final days of freedom before the accused was arrested in Berlin. He appeared in person at the trial and wants the Canadian courts to refund his cab ride to the airport in the German capital.
He also wants payment for alleged lost wages and the equivalent of 350 euros (about $500) to pay for a dog-watcher in Berlin.
"I can't for a minute support this man's word on these matters," Bouthillier said, adding he has no way of knowing if the receipts are real.
Montreal police, meanwhile, are seeking $100 they say they fronted Rubert for meals while he was in the city.
At one point Wednesday, Cournoyer stood up and walked behind the door through he which he enters the courtoom and began shouting at a group of court staff who were laughing and chatting.
The judge returned to the courtroom and noted one of the group of people he had just scolded was his own boss — the Superior Court chief justice.
Cournoyer noted the people in question likely didn't know the court was in session as everyone is usually at lunch at that hour.
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