The Brisbane Supreme Court jury asked for clarification about using circumstantial evidence to reach a verdict on Monday afternoon, shortly before they were sent home at the end of a third day of deliberations.
Jurors have now spent more than 19 hours trying to decide whether the 43-year-old murdered his wife in April 2012.
On Monday afternoon Supreme Court Justice John Byrne said he'd received a note asking for another reading of the "process, meaning and application of circumstantial evidence to arrive at a verdict".
Justice Byrne repeated his directions last week that circumstantial evidence was evidence that pointed to facts rather than proving them directly.
"As no one claims to have seen the accused kill his wife, this is a circumstantial case," he said.
To reach a guilty verdict based on circumstantial evidence guilt "must be the only rational inference that could be drawn from the circumstances", he added.
"If there is any reasonable possibility consistent with innocence, it is your duty to find the accused not guilty," he told the jury.
"This follows from the requirement that guilt must be established beyond reasonable doubt".
Jurors left court shortly after the clarification on Monday afternoon and will return for a forth day of deliberations on Tuesday.
Allison Baden-Clay's body was found on a creek bank at Anstead in Brisbane's west on April 30, 2012.
The discovery came ten days after her husband reported her missing from their home in nearby Brookfield.
Baden-Clay has pleaded not guilty to murder in a long-running trial that entered its sixth week on Monday.
Prosecutors say the former real estate agent probably smothered his wife at their house and dumped her body where it was found under the Kholo Creek Bridge.
They say he was under significant personal and financial pressure and had promised his mistress he'd be separated by July 1 that year.
In the witness box Baden-Clay vehemently denied the accusations and said he had been working on his marriage and had no plans to leave his wife.
His defence team suggested Allison Baden-Clay took her own life or died accidentally after wandering off at night.
Details of Baden-Clay's multiple affairs, his financial woes and Allison's history of depression were laid bare before a packed court during trial, which entered its sixth week on Monday.
About 180 items were submitted as evidence, including photographs of injuries on Baden-Clay's face that he said were shaving cuts from a blunt razor.
The court also heard police found Allison's blood in one of the couple's cars.
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