Following a lengthy summary from Judge Jonathan Williams, the panel of five women and seven men retired about 3.20pm (AEST) on Tuesday.
The 25-year-old Manly Sea Eagles fullback is charged with sexually assaulting and twice indecently assaulting a 17-year-old girl outside his north Manly home on March 6, 2009.
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The allegations include that he digitally penetrated the girl and tongue-kissed her.
Stewart's trial reached its tenth day on Tuesday at Sydney's Downing Centre District Court, hearing from scores of witnesses, including the alleged victim.
Teammates, friends and family gave character references for Stewart, while medical experts gave conflicting theories as to how the complainant came to have an area of redness near her vagina.
"People do hear, see and remember things differently from one person to another," Judge Williams told the jury before they retired.
He asked them to return with a unanimous verdict.
