Magnotta is charged with first-degree murder and four other charges in the slaying and dismemberment of Chinese engineering student Jun Lin in May 2012.
The eight women and four men officially began their work Tuesday to return five unanimous verdicts in the case. In theory, they will be deliberating between 9 a.m. and 5 p.m.
There was no word from them other than when they took breaks and they will return on Wednesday morning.
Magnotta has pleaded not guilty by way of mental disorder and is seeking to be found not criminally responsible.
On the murder charge, the jury has four options: find Magnotta guilty of first-degree murder, second-degree murder or manslaughter, or find him not criminally responsible by way of mental disorder.
The judge told the jurors Monday that if they find the accused not criminally responsible, that verdict must carry through to all five charges.
On the other charges, they must decide simply whether Magnotta is guilty or not guilty.
Quebec Superior Court Justice Guy Cournoyer suggested they start their work by focusing on the mental disorder defence.
The jurors heard some 66 witnesses over 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.