Hernandez's lead prosecutor said he plans to file a motion to recuse Bristol County Superior Court Judge Susan Garsh, with whom he has clashed in the past.
Garsh said she would schedule a separate hearing. Assistant district attorney William McCauley requested a confidential sidebar on the request, but Garsh denied the request.
McCauley blasted Garsh after a 2010 murder trial, saying that the judge showed "antagonism" toward the government.
Garsh was assigned to the case two weeks ago after Hernandez pleaded not guilty to an indictment charging him with the first-degree murder of Odin Lloyd, a 27-year-old semi-pro football player.
The recusal request is risky, because if it is not granted, the judge may react badly.
"Nobody like to be accused or suggested or being unfair or biased, so that can irritate a judge, who might react negatively," said David Siegel, a professor at the New England School of Law.
"On the other hand, knowing that allegation is out there might make someone be double, super, extra-sure that they don't appear partial and that could maybe have the effect of making some rulings go your way."
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